Rounds Of Editing Research Articles

Preoperative Counseling and Surgical Practice: Gynecologic Surgeons' Approach to Ovary-Sparing Hysterectomy [ID 2683432

INTRODUCTION: Since the early 20th century, surgical practices on prophylactic oophorectomy at the time of hysterectomy have fluctuated. This study aims to assess how current gynecologic surgeons are counseling patients on ovary-sparing benign hysterectomies and assess any gaps in provider knowledge. METHODS: Institutional review board exception was obtained. A survey was piloted and underwent several rounds of editing before being sent to members of American Association of Gynecologic Laparoscopists (AAGL) in April 2023. The questionnaire evaluated preoperative counseling on risks and benefits of ovary-sparing hysterectomy for benign indications and surgical practices for when to perform bilateral salpingectomy and oophorectomy. Descriptive statistics and regression analyses were performed. RESULTS: The survey was sent out by email to 6,622 AAGL members, 3,576 opened the email, and 520 completed surveys (14% response rate). Approximately one-half (58%) completed subspeciality training. Most counsel patients on the benefits of ovarian conservation including the prevention of osteoporosis (88%), early onset menopause (87%), cardiovascular disease (84%), and dementia (52%). Fifty percent recommend routine bilateral salpingo-oophorectomy at time of hysterectomy starting at age 61, whereas 38% recommend this be performed at age 51–55 years. CONCLUSION: Gynecologic surgeons are counseling patients on the risks and benefits of ovarian conservation. How frequently ovary-sparing hysterectomies are offered and the age at which bilateral salpingo-oophorectomy is recommended vary by provider. Additional high-quality studies are needed to further understand the optimal timing of oophorectomy at time of benign hysterectomy, and there is also a need for provider education to minimize discrepancy in practice patterns.

CRISPR/Cas12a toolbox for genome editing in Methanosarcina acetivorans.

Methanogenic archaea play an important role in the global carbon cycle and may serve as host organisms for the biotechnological production of fuels and chemicals from CO2 and other one-carbon substrates. Methanosarcina acetivorans is extensively studied as a model methanogen due to its large genome, versatile substrate range, and available genetic tools. Genome editing in M. acetivorans via CRISPR/Cas9 has also been demonstrated. Here, we describe a user-friendly CRISPR/Cas12a toolbox that recognizes T-rich (5'-TTTV) PAM sequences. The toolbox can manage deletions of 3,500 bp (i.e., knocking out the entire frhADGB operon) and heterologous gene insertions with positive rates of over 80%. Cas12a-mediated multiplex genome editing was used to edit two separate sites on the chromosome in one round of editing. Double deletions of 100 bp were achieved, with 8/8 of transformants being edited correctly. Simultaneous deletion of 100 bp at one site and replacement of 100 bp with the 2,400 bp uidA expression cassette at a separate site yielded 5/6 correctly edited transformants. Our CRISPR/Cas12a toolbox enables reliable genome editing, and it can be used in parallel with the previously reported Cas9-based system for the genetic engineering of the Methanosarcina species.

Documentation in Pediatric Microlaryngoscopy/Bronchoscopy: International Modified Delphi Consensus.

Complete and accurate documentation of surgical procedures is essential for optimizing patient care, yet significant variation in operative notes persists within and across institutions. We sought to reach consensus on the most important components of an operative note for pediatric microlaryngoscopy and bronchoscopy. A modified Delphi consensus process was used. A checklist for operative documentation, created by fellowship-trained pediatric otolaryngologists-head and neck surgeons, was sent to surgeons identified as experts in pediatric laryngoscopy and bronchoscopy. In the first round, items were rated as "keep" or "remove". In the second round, each item was rated on a 7-point Likert scale for importance. The mean score of each item was calculated to determine if consensus was reached. Overall, 43/74 (58.1%) surgeons responded to our survey. After two rounds of editing, 28 components reached consensus, 24 were near consensus, and 26 did not reach consensus. Items that reached final consensus had mean (SD) ratings of 6.12 (0.94) (range, 5.31-6.72). Pediatric otolaryngologists identified as bronchoscopy experts were able to create a checklist of essential components of an operative note for pediatric laryngoscopy and bronchoscopy using a Delphi method. Items reaching consensus included procedure name, description of breathing, grade of airway view, description of normal anatomic structures, grade of subglottic stenosis if present, presence and description of tracheobronchomalacia, presence of fistulae, cleft and rings, and several special cases including foreign body and tracheostomy management, as well as end of procedure disposition and complications. 5 Laryngoscope, 133:1234-1238, 2023.

Exploring collaborative caption editing to augment video-based learning.

Captions play a major role in making educational videos accessible to all and are known to benefit a wide range of learners. However, many educational videos either do not have captions or have inaccurate captions. Prior work has shown the benefits of using crowdsourcing to obtain accurate captions in a cost-efficient way, though there is a lack of understanding of how learners edit captions of educational videos either individually or collaboratively. In this work, we conducted a user study where 58 learners (in a course of 387 learners) participated in the editing of captions in 89 lecture videos that were generated by Automatic Speech Recognition (ASR) technologies. For each video, different learners conducted two rounds of editing. Based on editing logs, we created a taxonomy of errors in educational video captions (e.g., Discipline-Specific, General, Equations). From the interviews, we identified individual and collaborative error editing strategies. We then further demonstrated the feasibility of applying machine learning models to assist learners in editing. Our work provides practical implications for advancing video-based learning and for educational video caption editing.

Metabolic engineering of Escherichia coli BL21 strain using simplified CRISPR-Cas9 and asymmetric homology arms recombineering

BackgroundThe recent CRISPR-Cas coupled with λ recombinase mediated genome recombineering has become a common laboratory practice to modify bacterial genomes. It requires supplying a template DNA with homology arms for precise genome editing. However, generation of homology arms is a time-consuming, costly and inefficient process that is often overlooked.ResultsIn this study, we first optimized a CRISPR-Cas genome engineering protocol in the Escherichia coli (E. coli) BL21 strain and successfully deleted 10 kb of DNA from the genome in one round of editing. To further simplify the protocol, asymmetric homology arms were produced by PCR in a single step with two primers and then purified using a desalting column. Unlike conventional homology arms that are prepared through overlapping PCR, cloning into a plasmid or annealing synthetic DNA fragments, our method significantly both shortened the time taken and reduced the cost of homology arm preparation. To test the robustness of the optimized workflow, we successfully deleted 26 / 27 genes across the BL21 genome. Noteworthy, gRNA design is important for the CRISPR-Cas system and a general heuristic gRNA design has been proposed in this study. To apply our established protocol, we targeted 16 genes and iteratively deleted 7 genes from BL21 genome. The resulting strain increased lycopene yield by ~ threefold.ConclusionsOur work has optimized the homology arms design for gene deletion in BL21. The protocol efficiently edited BL21 to improve lycopene production. The same workflow is applicable to any E. coli strain in which genome engineering would be useful to further increase metabolite production.

Helicase-AID: A novel molecular device for base editing at random genomic loci

CRISPR-enabled deaminase base editing has become a powerful tool for precisely editing nucleotides on the chromosome. In this study DNA helicases, such as Escherichia coli DnaB, were fused to activation-induced cytidine deaminase (AID) to form enzyme complexes which randomly introduces edited bases throughout the chromosome. DnaB-AID was found to increase 2.5 × 103 fold relative to the mutagenesis frequency of wildtype. 97.9% of these edits were observed on the leading strand during DNA replication suggesting deamination to be highly coordinated with DNA replication. Using DnaB-AID, a 371.4% increase in β-carotene production was obtained following four rounds of editing. In Saccharomyces cerevisiae Helicase-AID was constructed by fusing AID to one of the subunits of eukaryotic helicase Mcm2-7 complex, MCM5. Using MCM5-AID, the average editing efficiency of five strains was 2.1 ± 0.4 × 103 fold higher than the native genomic mutation rate. MCM5-AID was able to improve β-carotene production of S. cerevisiae 4742crt by 75.4% following eight rounds of editing. The S. cerevisiae MCM5-AID technique is the first biological tool for generating and accumulating single base mutations in eukaryotic chromosomes. Since the helicase complex is highly conservative in all eukaryotes, Helicase-AID could be adapted for various applications and research in all eukaryotic cells.

Perioperative management and anaesthetic considerations in pelvic exenterations using Delphi methodology: results from the PelvEx Collaborative.

BackgroundThe multidisciplinary perioperative and anaesthetic management of patients undergoing pelvic exenteration is essential for good surgical outcomes. No clear guidelines have been established, and there is wide variation in clinical practice internationally. This consensus statement consolidates clinical experience and best practice collectively, and systematically addresses key domains in the perioperative and anaesthetic management.MethodsThe modified Delphi methodology was used to achieve consensus from the PelvEx Collaborative. The process included one round of online questionnaire involving controlled feedback and structured participant response, two rounds of editing, and one round of web-based voting. It was held from December 2019 to February 2020. Consensus was defined as more than 80 per cent agreement, whereas less than 80 per cent agreement indicated low consensus.ResultsThe final consensus document contained 47 voted statements, across six key domains of perioperative and anaesthetic management in pelvic exenteration, comprising preoperative assessment and preparation, anaesthetic considerations, perioperative management, anticipating possible massive haemorrhage, stress response and postoperative critical care, and pain management. Consensus recommendations were developed, based on consensus agreement achieved on 34 statements.ConclusionThe perioperative and anaesthetic management of patients undergoing pelvic exenteration is best accomplished by a dedicated multidisciplinary team with relevant domain expertise in the setting of a specialized tertiary unit. This consensus statement has addressed key domains within the framework of current perioperative and anaesthetic management among patients undergoing pelvic exenteration, with an international perspective, to guide clinical practice, and has outlined areas for future clinical research.

Ecology and Ethnogenesis: An Environmental History of the Wind River Shoshones, 1000–1868

In Ecology and Ethnogenesis, Adam R. Hodge presents a deep history of an Indigenous community too often overlooked by historians. This is a book of remarkable depth that tracks a group of people as they morphed culturally and politically during nearly a millennium. The book focuses on this group’s transformation from the Numu, the Eastern Shoshones, to the Wind River Shoshones over the course of that thousand-year span. Hodge argues that movement between vastly different ecologies prior to arrival of European colonists, as well as the changes to those environments wrought by European colonialism, played key roles in the development of modern Wind River Shoshone society. It is fundamentally an environmental history, showing how one Indigenous society’s environmental context, and their adaptation to ecological changes, shaped their social and cultural structure. “If we hope to grasp [the Wind River Shoshones’] past,” Hodge writes, “it is especially important to explore the interplay between their ancestors and the physical environments that they historically utilized” (3).The focus on the intersection of culture and ecology is well maintained throughout the book but is particularly strong in Hodge’s analysis of changing gender norms and roles within Eastern and Wind River Shoshone society. Hodge provides sensitive and nuanced discussions of polygyny and plural marriage among the Shoshones, arguing that such practices served important economic roles. “Gender complementarity and the practice of polygyny distributed critical labor practices and helped ensure productive Shoshone households and communities” during the high era of the mountain western fur trade in the early nineteenth century, Hodge argues (216–17). Gender is a major theme in this work as, in the author’s words, “ecological interrelationships that contributed to Eastern Shoshone distinctiveness often manifested in the form of gender dynamics. . . . I strive for a ‘genuine incorporation’ of Indian women’s history” (9). In this, Hodge succeeds wonderfully.Ecology and Ethnogenesis could have used another round of editing. This is not merely a matter of aesthetics—though, to be sure, word and phrase repetition can be distracting in the text. Some sentences and paragraphs run on long enough to obscure the central point the author is making, and unnecessarily wordy phrases similarly cloud meaning throughout the book. To cite one example of unnecessarily bulky sentences, in an early chapter Hodge writes: “The far northwestern portion of the Great Plains, a vast area that encompasses the grasslands of present-day Montana and Alberta, situated between the Yellowstone River on the south and the North Saskatchewan to the north, pulled Numic-speaking peoples northward along the eastern foot of the Northern Rockies because it afforded tremendous hunting opportunities” (86). Sentences of this size abound and do not clarify the story Hodge tells. This is a relatively minor drawback, but a noticeable one nonetheless.Adam Hodge’s Ecology and Ethnogenesis is a strong work of history, and the author’s emphasis on precontact Numu society and on the relationship between ecological change and gender history are welcome emphases in a field that too often ignores both. While some dense and occasionally unclear writing may mean this work appeals to a strictly academic audience, it will be of considerable use to any scholar working on the history of the North American West and those who have called that place home.

The Definitive Editor: Alfred Kreymborg and the Others Magazine-Anthology Duo

This article examines two intrinsically linked periodical publications: Others: A Magazine of the New Verse (1915–1919) and Others: An Anthology of the New Verse (1916–1920) both edited by Alfred Kreymborg. To date, scholarship on the publications has focused either on the magazine or, to a lesser extent, on the anthology, but never on the dynamic between the two publications. The article begins by considering the way both publications challenged the boundaries of medial form in an effort to better characterize the respective functions of the magazine and the anthology in the Others dynamic. It demonstrates how the anthology, an annual publication, allowed Kreymborg to reclaim editorial agency over the Others brand, facilitating a secondary round of editing of the magazine's contents. By creating a secondary selection of poems increasingly collated by guest editors, Kreymborg was able to further shape the representation of the duo. The restoration of the Others anthology to the history of the Others project sheds new light on key contributors and resultantly requires us to further nuance our understanding of the Others magazine as a largely inclusive project. In uncovering the role the Others anthology played in the Others dynamic, this article ultimately underscores the need to include the serially published modernist anthology in our understanding of the diverse and interrelated modernist media ecology.

Individual and combined presenilin 1 and 2 knockouts reveal that both have highly overlapping functions in HEK293T cells

Presenilins 1 and 2 (PS1 and 2) are the catalytic subunits of γ-secretase, a multiprotein protease that cleaves amyloid protein precursor and other type I transmembrane proteins. Previous studies with mouse models or cells have indicated differences in PS1 and PS2 functions. We have recently reported that clinical γ-secretase inhibitors (GSIs), initially developed to manage Alzheimer's disease and now being considered for other therapeutic interventions, are both pharmacologically and functionally distinct. Here, using CRISPR/Cas9-based gene editing, we established human HEK 293T cell lines in which endogenous PS1, PS2, or both have been knocked out. Using these knockout lines to examine differences in PS1- and PS2-mediated cleavage events, we confirmed that PS2 generates more intracellular β-amyloid than does PS1. Moreover, we observed subtle differences in PS1- and PS2-mediated cleavages of select substrates. In exploring the question of whether differences in activity among clinical GSIs could be attributed to differential inhibition of PS1 or PS2, we noted that select GSIs inhibit PS1 and PS2 activities on specific substrates with slightly different potencies. We also found that endoproteolysis of select PS1 FAD-linked variants in human cells is more efficient than what has been previously reported for mouse cell lines. Overall, these results obtained with HEK293T cells suggest that selective PS1 or PS2 inhibition by a given GSI does not explain the previously observed differences in functional and pharmacological properties among various GSIs.

Consensus statement on the multidisciplinary management of patients with recurrent and primary rectal cancer beyond total mesorectal excision planes

The management of primary rectal cancer beyond total mesorectal excision planes (PRC-bTME) and recurrent rectal cancer (RRC) is challenging. There is global variation in standards and no guidelines exist. To achieve cure most patients require extended, multivisceral, exenterative surgery, beyond conventional total mesorectal excision planes. The aim of the Beyond TME Group was to achieve consensus on the definitions and principles of management, and to identify areas of research priority. Delphi methodology was used to achieve consensus. The Group consisted of invited experts from surgery, radiology, oncology and pathology. The process included two international dedicated discussion conferences, formal feedback, three rounds of editing and two rounds of anonymized web-based voting. Consensus was achieved with more than 80 per cent agreement; less than 80 per cent agreement indicated low consensus. During conferences held in September 2011 and March 2012, open discussion took place on areas in which there is a low level of consensus. The final consensus document included 51 voted statements, making recommendations on ten key areas of PRC-bTME and RRC. Consensus agreement was achieved on the recommendations of 49 statements, with 34 achieving consensus in over 95 per cent. The lowest level of consensus obtained was 76 per cent. There was clear identification of the need for referral to a specialist multidisciplinary team for diagnosis, assessment and further management. The consensus process has provided guidance for the management of patients with PRC-bTME or RRC, taking into account global variations in surgical techniques and technology. It has further identified areas of research priority.

Consensus statement on the multidisciplinary management of patients with recurrent and primary rectal cancer beyond total mesorectal excision planes

The management of primary rectal cancer beyond total mesorectal excision planes (PRC-bTME) and recurrent rectal cancer (RRC) is challenging. There is global variation in standards and no guidelines exist. To achieve cure most patients require extended, multivisceral, exenterative surgery, beyond conventional total mesorectal excision planes. The aim of the Beyond TME Group was to achieve consensus on the definitions and principles of management, and to identify areas of research priority. Delphi methodology was used to achieve consensus. The Group consisted of invited experts from surgery, radiology, oncology and pathology. The process included two international dedicated discussion conferences, formal feedback, three rounds of editing and two rounds of anonymized web-based voting. Consensus was achieved with more than 80 per cent agreement; less than 80 per cent agreement indicated low consensus. During conferences held in September 2011 and March 2012, open discussion took place on areas in which there is a low level of consensus. The final consensus document included 51 voted statements, making recommendations on ten key areas of PRC-bTME and RRC. Consensus agreement was achieved on the recommendations of 49 statements, with 34 achieving consensus in over 95 per cent. The lowest level of consensus obtained was 76 per cent. There was clear identification of the need for referral to a specialist multidisciplinary team for diagnosis, assessment and further management. The consensus process has provided guidance for the management of patients with PRC-bTME or RRC, taking into account global variations in surgical techniques and technology. It has further identified areas of research priority.

The Revised Research Agenda for Physical Therapy

In its recent history, the physical therapy profession embarked on at least 2 attempts to create a research agenda. The first attempt occurred in December 1993 when a panel of researchers representing different clinical foci and levels of expertise was convened to develop an agenda. This effort was not as successful as hoped because the panel could not reach consensus on an agenda that would benefit the profession as a whole. The conclusion was reached that all researchers' programs of research were important; thus, no decisions were made to prescribe a program of research for the profession. Despite this unremarkable outcome, the profession initiated a second attempt to create an agenda. Beginning in 1998, a call was placed to presidents of all components (ie, chapters and sections) of the American Physical Therapy Association (APTA), academic administrators of physical therapist education programs, and members of the Section on Research asking for nominations of individuals to participate in the development of a Clinical Research Agenda. Ultimately, 48 nominated individuals were selected. Two meetings were held, one in the fall and the second in the winter of 1998. Additionally, an Editorial Advisory Panel (EAP) met between the 2 meetings. The EAP, as its name implies, edited the output from the first meeting and presented it for discussion during the second meeting. Subsequent to the second conference and a second round of editing by the EAP, the 128 research questions comprising the draft agenda were sent to a sample of APTA membership for final review. Subsequent to the second review and the results of an algorithm to determine which items would be maintained, 72 questions were incorporated into the final agenda. Ultimately, the Clinical Research Agenda was published in Physical Therapy 1 so that it could be widely disseminated to the community of scientists …

The Power of Plagues

The purpose of this book is to make the science of epidemic diseases accessible and understandable; to guide the general reader through the maze of contagious diseases, their past importance, the means by which we came to understand them, and how they may affect our future. This commentary on general and disease-specific concerns covers the nature of plagues; plagues, the price of being sedentary (an evolutionary view); 6 plagues of antiquity (urinary schistosomiasis, the plague of Athens, malaria in Rome, the Antonine plague, the plagues of Cyprian and Justinian); bubonic plague; AIDS (including a history of virology and an account of leukocyte function); typhus; malaria (plus an explanation of sickle cell disease and genetics); cholera; smallpox; preventing plagues (the immune system, with a coda on vaccine development); the plague protectors (antisepsis and antimicrobial drugs); syphilis; tuberculosis; leprosy; 6 plagues of Africa (sleeping sickness, river blindness, guinea worm, yellow fever, malaria, and hookworm) with the history of exploration and exploitation of this continent; plagues without germs (pellagra, beriberi, scurvy, and rickets); and emerging plagues (rodentborne, West Nile virus, bovine spongiform encephalopathy and Creutzfeldt-Jakob disease, and influenza). The text covers not only the geography, history, microbiology, and physiology of these infections but also their influence on plastic art, movies, literature, and music (with a special fondness for nursery rhymes). Surprisingly, the role of contemporary epidemiologic methods and governmental institutions is not examined. No explanation is included of how present-day public health officials go about detecting a problem, how they define an epidemic, how they use data such as incidence or attack rates to identify the cause, and how laws and regulations (e.g., vaccine requirements for school entry and rules for production of food and biological materials) are indispensable for disease prevention. The text would have profited from another round of editing to modify overly forceful generalizations, tighten the discussion, and check for historical and medical accuracy. For example, acyclovir is not AZT, and AZT was not available for first-line treatment of AIDS in the early 1980s; cholera is not slowly creeping into the Western Hemisphere, but it produced large epidemics in Central and South America in the 1990s; Figure 9.7B is not an antivaccination statement from Boston in 1902 but, as the engraving itself indicates, a provaccine statement from England in 1898; vaccination with Mycobacterium bovis BCG does not cause the tuberculin test result to be negative; and malaria control efforts in the United States were not interrupted by World War II but, on the contrary, were enhanced by the creation of an agency called Malaria Control in War Areas. This is a concise and clear account of the biologic and historical determinants of epidemic diseases. It is marred by a small number of factual errors and a failure to include epidemiologic and public health methods as components of the equation that determines the power of plagues.

Trypanosome U-deletional RNA editing involves guide RNA-directed endonuclease cleavage, terminal U exonuclease, and RNA ligase activities.

We have studied the mechanism of accurate in vitro RNA editing of Trypanosoma brucei ATPase 6 mRNA, using four mRNA-guide RNA (gRNA) pairs that specify deletion of 2, 3, or 4 U residues at editing site 1 and mitochondrial extract. This extract not only catalyzes deletion of the specified number of U residues but also exhibits a novel endonuclease activity that cleaves the input pre-mRNA in a gRNA-directed manner, precisely at the phosphodiester bond predicted in a simple enzymatic model of RNA editing. This cleavage site is inconsistent with a chimera-based editing mechanism. The U residues to be deleted, present at the 3' end of the upstream cleavage product, are then removed evidently by a 3' U-specific exonuclease and not by a reverse reaction of terminal U transferase. RNA ligase can then join the mRNA halves through their newly formed 5' P and 3' OH termini, generating mRNA faithfully edited at the first editing site. This resultant, partially edited mRNA can then undergo accurate, gRNA-directed cleavage at editing site 2, again precisely as predicted by the enzymatic editing model. All of these enzymatic activities cofractionate with the U-deletion activity and may reside in a single complex. The data imply that each round of editing is a four-step process, involving (i) gRNA-directed cleavage of the pre-mRNA at the bond immediately 5' of the region base paired to the gRNA, (ii) U deletion from or U addition to the 3' OH of the upstream mRNA half, (iii) ligation of the mRNA halves, and (iv) formation of additional base pairing between the correctly edited site and the gRNA that directs subsequent nuclease cleavage at the next editing site.