bluuebunny/crossref_metadata_2025 huggingface dataset:
QTL mapping of a Brazilian bioethanol strain links the cell wall protein-encoding gene GAS1 to low pH tolerance in S. cerevisiae
Authors: Coradini Alessandro L. V. , da Silveira Bezerra de Mello Fellipe , Furlan Monique , Maneira Carla , Carazzolle Marcelo F. , Pereira Gonçalo Amarante Guimaraes , Teixeira Gleidson Silva
Published: December 2021

Background

Saccharomyces cerevisiaeis largely applied in many biotechnological processes, from traditional food and beverage industries to modern biofuel and biochemicals factories. During the fermentation process, yeast cells are usually challenged in different harsh conditions, which often impact productivity. Regarding bioethanol production, cell exposure to acidic environments is related to productivity loss on both first- and second-generation ethanol. In this scenario, indigenous strains traditionally used in fermentation stand out as a source of complex genetic architecture, mainly due to their highly robust background—including low pH tolerance.

Results

In this work, we pioneer the use of QTL mapping to uncover the genetic basis that confers to the industrial strain Pedra-2 (PE-2) acidic tolerance during growth at low pH. First, we developed a fluorescence-based high-throughput approach to collect a large number of haploid cells using flow cytometry. Then, we were able to apply a bulk segregant analysis to solve the genetic basis of low pH resistance in PE-2, which uncovered a region in chromosome X as the major QTL associated with the evaluated phenotype. A reciprocal hemizygosity analysis revealed the alleleGAS1, encoding a β-1,3-glucanosyltransferase, as the casual variant in this region. TheGAS1sequence alignment of distinctS. cerevisiaestrains pointed out a non-synonymous mutation (A631G) prevalence in wild-type isolates, which is absent in laboratory strains. We further showcase thatGAS1allele swap between PE-2 and a low pH-susceptible strain can improve cell viability on the latter of up to 12% after a sulfuric acid wash process.

Conclusion

This work revealedGAS1as one of the main causative genes associated with tolerance to growth at low pH in PE-2. We also showcase howGAS1PE-2can improve acid resistance of a susceptible strain, suggesting that these findings can be a powerful foundation for the development of more robust and acid-tolerant strains. Our results collectively show the importance of tailored industrial isolated strains in discovering the genetic architecture of relevant traits and its implications over productivity.
Accurate prediction of acute pancreatitis severity based on genome-wide cell free DNA methylation profiles
Authors: Sun Hong-Wei , Dai Sheng-Jie , Kong Hong-Ru , Fan Jie-Xiang , Yang Fang-Yuan , Dai Ju-Qing , Jin Yue-Peng , Yu Guan-Zhen , Chen Bi-Cheng , Shi Ke-Qing
Published: December 2021

Background

Patients with severe acute pancreatitis (SAP) have a high mortality, thus early diagnosis and interventions are critical for improving survival. However, conventional tests are limited in acute pancreatitis (AP) stratification. We aimed to assess AP severity by integrating the informative clinical measurements with cell free DNA (cfDNA) methylation markers.

Methods

One hundred and seventy-five blood samples were collected from 61 AP patients at multiple time points, plus 24 samples from healthy individuals. Genome-wide cfDNA methylation profiles of all samples were characterized with reduced representative bisulfite sequencing. Clinical blood tests covering 93 biomarkers were performed on AP patients within 24 h. SAP predication models were built based on cfDNA methylation and conventional blood biomarkers separately and in combination.

Results

We identified 565 and 59 cfDNA methylation markers informative for acute pancreatitis and its severity. These markers were used to develop prediction models for AP and SAP with area under the receiver operating characteristic of 0.92 and 0.81, respectively. Twelve blood biomarkers were systematically screened for a predictor of SAP with a sensitivity of 87.5% for SAP, and a specificity of 100% in mild acute pancreatitis, significantly higher than existing blood tests. An expanded model integrating 12 conventional blood biomarkers with 59 cfDNA methylation markers further improved the SAP prediction sensitivity to 92.2%.

Conclusions

These findings have demonstrated that accurate prediction of SAP by the integration of conventional and novel blood molecular markers, paving the way for early and effective SAP intervention through a non-invasive rapid diagnostic test.
COVID-19 and chronic diabetes: the perfect storm for reactivation tuberculosis?: a case series
Authors: Aguillón-Durán Genesis P. , Prieto-Martínez Ericka , Ayala Doris , García Juan , Thomas John M. , García Juan Ignacio , Henry Brandon Michael , Torrelles Jordi B. , Turner Joanne , Ledezma-Campos Eder , Restrepo Blanca I.
Published: December 2021

Background

The coronavirus disease 2019 pandemic is predicted to have a net negative effect on tuberculosis control, with an estimated excess of 6.3 million tuberculosis cases and 1.4 million deaths by 2025. Programmatic issues such as the lockdown of tuberculosis services affect all patients, while biosocial factors have a differential impact on an individual’s risk for tuberculosis or adverse tuberculosis outcomes.

Case presentation

We report three Hispanic cases of incident tuberculosis (two males, 43 and 44 years old; one female, 49 years old) after resolution of coronavirus disease episodes. Coincidentally, all cases shared a common risk factor: a chronic history poorly controlled diabetes.

Conclusions

Our findings alert to the threat posed by the synergy between coronavirus disease and diabetes, on tuberculosis reactivation. In medium- to high-risk settings for tuberculosis, we recommend implementation of routine screening for latent tuberculosis infection in these cases, and preventive tuberculosis treatment in those who are positive.
ViaFuse: Fiji macros to calculate skeletal muscle cell viability and fusion index
Authors: Hinkle Emma Rose , Essader Tasneem Omar , Gentile Gabrielle Marie , Giudice Jimena
Published: December 2021

Background

Measuring biological features of skeletal muscle cells is difficult because of their unique morphology and multinucleate nature upon differentiation. Here, we developed a new Fiji macro package called ViaFuse (that stands for viability and fusion) to measure skeletal muscle cell viability and differentiation. To test ViaFuse, we utilized immunofluorescence images of differentiated myotubes where the capping actin protein of muscle z-line subunit beta (CAPZB) was depleted in comparison with control cells.

Results

We compared the values achieved using the ViaFuse macros first with manual quantification performed by researchers and second with those obtained utilizing the MATLAB muscle-centric software MyoCount. We observed a high degree of correlation between all methods of quantification.

Conclusions

ViaFuse can detect the borders of myotubes and identify nuclear clumps which have been limitations of previous muscle-centric imaging software. The ViaFuse macros require little computer power or space to run and user inputs to the ViaFuse macros are minimal, thereby automating the analysis process in a quick, easy, and accurate fashion. Additionally, the ViaFuse macros work with Fiji, an existing imaging software widely used by skeletal muscle researchers. Furthermore, ViaFuse is compatible with many computer systems, has a very intuitive interface, and does not require prior complex mathematical knowledge. Therefore, we propose ViaFuse as a robust and meticulous method to quantify skeletal muscle cell viability and differentiation.
Protocol for a systematic review and meta-analysis of studies on the use of brain natriuretic peptide and N-terminal brain natriuretic peptide levels in the diagnosis of cardiopulmonary edema in acute respiratory failure
Authors: Terayama Takero , Taniguchi Takuya , Imai Ryosuke , Anan Keisuke , Yoshida Takuo , Ando Koichi , Okamori Satoshi , Okada Yohei
Published: December 2021

Background

Dyspnea with bilateral pulmonary edema is common among patients in emergency departments (EDs) or intensive care units (ICUs). For the initial management of patients with this condition, cardiopulmonary edema (CPE) must be differentiated from acute respiratory distress syndrome (ARDS) in clinical settings. Brain natriuretic peptide (BNP) and N-terminal brain natriuretic peptide (NT-proBNP) are useful in distinguishing these conditions. However, current data about the use of these indexes are limited. Hence, we planned to perform a systematic review and meta-analysis to determine the accuracy of the two indexes for the diagnosis of CPE.

Methods

We designed and registered a study protocol for a systematic review and meta-analysis. This study aims to determine the diagnostic accuracy of BNP and NT-proBNP based on the standards of the methodology of the Cochrane Handbook for Systematic Reviews of Diagnostic Test Accuracy and the Preferred Reporting Items for a Systematic Review and Meta-analysis of Diagnostic Test Accuracy Studies in reporting the findings of this review. We will search PubMed (MEDLINE), Cochrane Library, Embase, www.ClinicalTrials.gov, International Clinical Trials Registry Platform, and Google Scholar. Randomized controlled trials, cross-sectional studies, and observational cohort studies reporting the accuracy in diagnosing CPE among adult patients with dyspnea and bilateral pulmonary edema will be included in the analysis. There will be no limits regarding language and publication date for this review. Two reviewers will independently screen articles, extract data, evaluate for quality and bias using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2), and use Grading of Recommendations Assessment, Development and Evaluation to summarize the strength of body of evidence. Then, a meta-analysis will be performed, and different statistical methods will be used to investigate heterogeneity among studies. A subgroup analysis of elderly patients with left ventricular dysfunction or chronic renal dysfunction will be performed. In the meta-analysis, a hierarchical summary receiver operating characteristic model or a bivariate model will be used in each index test, as appropriate.

Discussion

A systematic review and meta-analysis of the accuracy of BNP and NT-proBNP for the diagnosis of CPE will be conducted. The result of this study can help clinicians to identify an appropriate initial treatment for patients with acute respiratory failure, including those with ARDS and CPE. To the best of our knowledge, this will be the first comprehensive systematic review focusing on ARDS management in a specific population.

Systematic review registration

PROSPERO ID CRD42020201576
Two pulse intrusive events of the Pliocene Tanigawa-dake granites revealed from zircon U–Pb dating
Authors: Minami Saki , Nagata Mitsuhiro , Sueoka Shigeru , Fukuda Shoma , Kajita Yuya , Ogita Yasuhiro , Kagami Saya , Yokoyama Tatsunori , Tagami Takahiro
Published: December 2021

We performed zircon U–Pb dating on the Pliocene Tanigawa-dake granites (Makihata and Tanigawa bodies) and the Cretaceous Minakami quartzdiorite, Northeast Japan Arc. Concordia ages were estimated to be 3.95 ± 0.11 Ma (± 2 sigma) for the Makihata body, 3.18 ± 0.13 Ma and 3.32 ± 0.15 Ma for the Tanigawa body, and 109.4 ± 2.2 Ma for the Minakami quartzdiorite. The Minakami quartzdiorite is possibly correlated to the bedrock in the Ashio belt because the age of the Minakami quartzdiorite is consistent with the zircon U–Pb ages of the earliest Tadamigawa granites (107–62 Ma) which are distributed to the northeast of the Tanigawa-dake region and belong to the Ashio belt. All the zircon U–Pb ages of the Tanigawa-dake granites are older than the previously reported cooling ages, i.e., K–Ar ages and zircon fission-track ages, being consistent with their difference in closure temperature. On the basis of these results, we concluded that the intrusive ages of the Tanigawa-dake granites are ~ 4–3 Ma, which are among the youngest exposed plutons on Earth. The U–Pb ages of the Makihata body and the Tanigawa body are different significantly in the 2 sigma error range. Thus, the Tanigawa body intruded later than the Makihata body by ~ 0.7 Myr.

Graphical Abstract
Co-designing genomics research with a large group of donor-conceived siblings
Authors: Nunn Jack S. , Crawshaw Marilyn , Lacaze Paul
Published: December 2021

Background

Human genomics research is growing rapidly. More effective methods are required for co-design and involving people, especially those sub-populations which are inherently high interest to medical research and thus at greater risk of being exploited. This case study documents how we worked with a large group of donor-conceived siblings who share the same sperm donor father, to explore how they might want to engage with and influence any future genomic research.

Method

A participatory action research process was used to explore the views of a group of 18 people who knew they are donor-conceived siblings. They are part of a larger group of up to 1000 people who share the same sperm donor father but the only ones in contact with each other; it is likely that many of the uncontacted siblings are unaware of their biological father, have been unable to trace others or have died. The discussion explored views about how the group would like to be involved in future research. Five members participated in co-design; 12 completed a pre-discussion online survey; and six participated in an online discussion forum and evaluation survey. The online discussion was led by one facilitator, supported by the study team.

Results

Of the 18 siblings approached in 2018, 14 participated in the co-design stages or the surveys and online discussion. Co-design informed the research process. Participants reported enjoying the overall experience of the surveys and discussion forum, which were perceived as inclusive and flexible. Most participants’ views regarding the value of involvement in research changed during the process, and ‘widened’ about who should be involved. Participants were supportive of future research being done with the siblings group. All who completed the final survey requested to remain part of the co-design process. Other themes in the online discussion included concerns about conflicting interests and a desire for research participation to improve the situation for people affected by assisted conception. The process informed later discussions in the sibling group about participating in a self-managed biobank and informed decision making about participating in genomics research.

Conclusion

Findings from this study help inform ways in which people from certain sub-populations can be involved in planning and defining their participation in genomic research, particularly those that are inherently high interest to medical research and thus at greater risk of exploitation. This process provides a replicable method of involving potential participants in co-designing genomics research using online discussions, with positive outcomes. Reporting this study using ‘Standardised data on initiatives (STARDIT)’ to report the process allows comparison with other studies.
Potential field data interpolation by Taylor series expansion
Authors: Chen Tao , Yang Dikun
Published: December 2021

Data interpolation is critical in the analysis of geophysical data when some data are missing or inaccessible. We interpolate irregular or missing potential field data using the relation between adjacent data points inspired by the Taylor series expansion (TSE). The TSE method first finds the derivatives of a given point near the query point using data from neighboring points and then uses the Taylor series to obtain the value at the query point. The TSE method works by extracting local features represented as derivatives from the original data for interpolation in the area of data vacancy. Compared with other interpolation methods, the TSE provides a complete description of potential field data. Specifically, the remainder in TSE can measure local fitting errors and help obtain accurate results. Implementation of the TSE method involves two critical parameters — the order of the Taylor series and the number of neighbors used in the calculation of derivatives. We find that the first parameter must be carefully chosen to balance between the accuracy and numerical stability when data contain noise. The second parameter can help us build an over-determined system for improved robustness against noise. Methods of selecting neighbors around the given point using an azimuthally uniform distribution or the nearest-distance principle are also presented. Our approach is first illustrated by a synthetic gravity data set from a single survey line, and then it is generalized to the case over a survey grid. In both numerical experiments, the TSE method demonstrates an improved interpolation accuracy in comparison with the minimum curvature method. Finally, we apply the TSE method to a ground gravity data set from the Abitibi Greenstone Belt, Canada, and an airborne gravity gradient data set from the Vinton Dome, Louisiana, USA.
Ground-roll extraction using the Karhunen-Loeve transform in the time-frequency domain
Authors: Serdyukov Aleksander S.
Published: December 2021

Ground-roll suppression is critical for seismic reflection data processing. Many standard methods, i.e., f-k fan filtering, fail when spatially aliased surface wave interference is present in the data. Spatial aliasing is a common problem; receiver spacing is often not dense enough to extract wavenumbers of low-velocity surface waves. It has long been known that the Karhunen-Loeve (KL) transform can be used to suppress aliased ground roll. However, the ground roll should be flattened before suppression, which is challenging due to the dispersion of surface wave velocities. I propose to solve this problem via the time-frequency domain. I apply the S-transform, which was previously shown to perform well in the multichannel analysis of surface waves. A simple complex-valued constant phase shift is a suitable model of surface wave propagation in common-frequency S-transform gathers. Therefore, it is easy to flatten the corresponding S-transform narrow-band frequency surface wave packet and extract it from the data by principal component analysis of the corresponding complex-valued data-covariance matrix. As the result, our S-transform KL (SKL) method filters the aliased ground roll without damaging the reflection amplitudes. The advantages of SKL filtering have been confirmed by synthetic- and field-data processing.
Nonhyperbolic normal moveout stretch correction with deep learning automation
Authors: Abedi Mohammad Mahdi , Pardo David
Published: December 2021

Normal-moveout (NMO) correction is a fundamental step in seismic data processing. It consists of mapping seismic data from recorded traveltimes to corresponding zero-offset times. This process produces wavelet stretching as an undesired by-product. We have addressed the NMO stretching problem with two methods: (1) an exact stretch-free NMO correction that prevents the stretching of primary reflections and (2) an approximate post-NMO stretch correction. Our stretch-free NMO produces parallel moveout trajectories for primary reflections. Our post-NMO stretch correction calculates the moveout of stretched wavelets as a function of offset. Both methods are based on the generalized moveout approximation and are suitable for application in complex anisotropic or heterogeneous environments. We use new moveout equations, modify the original parameter functions to be a constant over the primary reflections, and then interpolate the seismogram amplitudes at the calculated traveltimes. For fast and automatic modification of the parameter functions, we use deep learning. We design a deep neural network (DNN) using convolutional layers and residual blocks. To train the DNN, we generate a set of 40,000 synthetic NMO-corrected common-midpoint gathers and the corresponding desired outputs of the DNN. The data set is generated using different velocity profiles, wavelets, and offset vectors, and it includes multiples, ground roll, and band-limited random noise. The simplicity of the DNN task — a 1D identification of primary reflections — improves the generalization in practice. We use the trained DNN and find successful applications of our stretch-correction method on synthetic and different real data sets.
Early Intervention in Psychosis services: A systematic review and narrative synthesis of the barriers and facilitators to implementation
Authors: O’Connell N. , O’Connor K. , McGrath D. , Vagge L. , Mockler D. , Jennings R. , Darker C. D.
Published: December 2021

Background

Early intervention in psychosis (EIP) services target the early manifestation of psychosis and provide multidisciplinary care. They demonstrate effectiveness and cost-effectiveness. Implementation of EIP services is inconsistent and piecemeal. This systematic review and narrative synthesis aims to identify barriers and facilitators to EIP service implementation.

Methods

We conducted an electronic search of databases (EMBASE, Medline, Web of Science, and PsychINFO) to detect papers reporting EIP service implementation findings and associated barriers and facilitators. The search occurred between June to August 2020, and again in January 2021. Articles meeting inclusion criteria were extracted and narratively synthesized. A quality assessment was conducted using the Mixed Methods Appraisal Tool.

Results

Twenty-three studies were selected. The most common study design was descriptive accounts of implementation. Patient age ranged varied from 14 to 35 years. We identified three barrier and facilitator domains: (a) system; (b) services; and (c) staff, and a range of subdomains. The most frequent subdomains were “funding” and “strength of collaboration and communication between EIP and outside groups and services”. Associations between domains and subdomains were evident, particularly between systems and services.

Conclusions

A range of barriers and facilitators to EIP implementation exist. Some of these are generic factors germane across health systems and services, while others are specific to EIP services. A thorough prior understanding of these challenges and enablers are necessary before implementation is attempted. Accounting for these issues within local and national contexts may help predict and increase the likelihood of services’ success, stability, and longevity.
Western Honduras Copán Population–Based Cancer Registry: Initial Estimates and a Model for Rural Central America
Authors: Norwood Dalton Argean , Montalvan-Sanchez Eleazar Enrique , Corral Juan E. , Estévez-Ordoñez Dagoberto , Paredes Andrea A. , Domínguez Lucia B. , Rodríguez Aida A. , Bravo Luis E. , Morgan Douglas R. , Domínguez Ricardo L.
Published: December 2021

PURPOSE

Population-based cancer registries (PBCRs) are critical for national cancer control planning, yet few low- and middle-income countries (LMICs) have quality PBCRs. The Central America Four region represents the principal LMIC region in the Western hemisphere. We describe the establishment of a PBCR in rural Western Honduras with first estimates for the 2013-2017 period.

METHODS

The Western Honduras PBCR was established through a collaboration of academic institutions and the Honduras Ministry of Health for collection of incident cancer data from public and private health services. Data were recorded using the Research Electronic Data Capture (REDCap) web-based platform with data monitoring and quality checks. Crude and age-standardized rates (ASRs) were calculated at the regional level, following WHO methodology.

RESULTS

The web-based platform for data collection, available ancillary data services (eg, endoscopy), and technical support from international centers (United States and Colombia) were instrumental for quality control. Crude cancer incidence rates were 112.2, 69.8, and 154.6 per 100,000 habitants overall, males, and females, respectively (excluding nonmelanoma skin cancer). The adjusted ASRs were 84.2, 49.6, and 118.9 per 100,000 overall habitants, males, and females, respectively. The most common sites among men were stomach (ASR 26.0, 52.4%), colorectal (ASR 5.11, 10.15%), and prostate (ASR 2.7, 5.4%). The most common sites in women were cervix (ASR 34.2, 36.7%), breast (ASR 11.2, 12.3%), and stomach (ASR 10.8, 11.7%).

CONCLUSION

The Copán-PBCR represents a successful model to develop cancer monitoring in rural LMICs. Innovations included the use of the REDCap platform and leverage of Health Ministry resources. This provides the first PBCR data for Honduras and the Central America Four and confirms that infection-driven cancers, such as gastric and cervical, should be priority targets for cancer control initiatives.
Single-Agent Mosunetuzumab Shows Durable Complete Responses in Patients With Relapsed or Refractory B-Cell Lymphomas: Phase I Dose-Escalation Study
Authors: Budde Lihua E. , Assouline Sarit , Sehn Laurie H. , Schuster Stephen J. , Yoon Sung-Soo , Yoon Dok Hyun , Matasar Matthew J. , Bosch Francesc , Kim Won Seog , Nastoupil Loretta J. , Flinn Ian W. , Shadman Mazyar , Diefenbach Catherine , O'Hear Carol , Huang Huang , Kwan Antonia , Li Chi-Chung , Piccione Emily C. , Wei Michael C. , Yin Shen , Bartlett Nancy L.
Published: December 2021

PURPOSE

Mosunetuzumab is a bispecific antibody targeting CD20 and CD3 that redirects T cells to engage and eliminate malignant B cells and is being developed for relapsed or refractory (R/R) B-cell non-Hodgkin lymphomas (B-NHLs).

METHODS

This first-in-human trial (ClinicalTrials.gov identifier: NCT02500407 ) evaluated the safety and tolerability and efficacy of mosunetuzumab in patients with R/R B-NHL and established the recommended phase II dose. Data from dose escalation are presented. Single-agent mosunetuzumab was administered intravenously in 3-week cycles, at full dose in cycle 1 day 1 (group A) or with ascending (step-up) doses during cycle 1 on days 1, 8, and 15 (group B), for eight or 17 cycles on the basis of tumor response.

RESULTS

Two hundred thirty patients were enrolled. Doses up to 2.8 mg and 60 mg were assessed in groups A and B, respectively; maximum tolerated dose was not exceeded. In group B (n = 197), common adverse events (≥ 20% of patients) were neutropenia (28.4%), cytokine release syndrome (27.4%), hypophosphatemia (23.4%), fatigue (22.8%), and diarrhea (21.8%). Cytokine release syndrome was mostly low-grade (grade ≥ 3: 1.0%) and mainly confined to cycle 1. Across the doses investigated (group B), best overall response rates were 34.9% and 66.2% in patients with aggressive and indolent B-NHL, respectively, and complete response rates were 19.4% and 48.5%. Among patients with a complete response, the median duration of response was 22.8 months (95% CI, 7.6 to not estimable) and 20.4 (95% CI, 16 to not estimable) in patients with aggressive and indolent B-NHL, respectively.

CONCLUSION

Mosunetuzumab, administered with step-up dosing, has a manageable safety profile and induces durable complete responses in R/R B-NHL. The expansion stage of the study is ongoing at the dose level of 1/2/60/60/30 mg selected for further study.
Two-Stage Single-Arm Trials Are Rarely Analyzed Effectively or Reported Adequately
Authors: Grayling Michael J. , Mander Adrian P.
Published: December 2021

PURPOSE

Two-stage single-arm designs have historically been the most common design used in phase II oncology. They remain a mainstay today, particularly for trials in rare subgroups. Consequently, it is imperative such studies be designed, analyzed, and reported effectively. We comprehensively review such trials to examine whether this is the case.

METHODS

Oncology trials that used Simon's two-stage design over a 5-year period were identified and reviewed. They were evaluated for whether they reported sufficient design (eg, required sample size) and analysis (eg, CI) details. Articles that did not adjust their inference for the incorporation of an interim analysis were also reanalyzed.

RESULTS

Four-hundred twenty-five articles were included. Of these, just 47.5% provided the five components that ensure design reproducibility. Only 1.2% and 2.1% reported an adjusted point estimate or CI, respectively. Just 55.3% provided the final stage rejection bound, indicating many trials did not test a hypothesis for their primary outcome. Trial reanalyses suggested reported point estimates underestimated treatment effects and reported CIs were too narrow.

CONCLUSION

Key design details of two-stage single-arm trials are often unreported. Their inference is rarely performed such as to remove bias introduced by the interim analysis. These findings are particular alarming when considered against the growing trend in which nonrandomized trials make up a large proportion of all evidence on a treatment's effectiveness in a rare biomarker-defined patient subgroup. Future studies must improve the way they are analyzed and reported.
Airway Ultrasound as Predictor of Difficult Direct Laryngoscopy: A Systematic Review and Meta-analysis
Authors: Carsetti Andrea , Sorbello Massimiliano , Adrario Erica , Donati Abele , Falcetta Stefano
Published: December 2021

BACKGROUND:

Despite several clinical index tests that are currently applied for airway assessment, unpredicted difficult laryngoscopy may still represent a serious problem in anesthesia practice. The aim of this systematic review and meta-analysis was to evaluate whether preoperative airway ultrasound can predict difficult direct laryngoscopy in adult patients undergoing elective surgery under general anesthesia.

METHODS:

We searched the Medline, Scopus, and Web of Science databases from their inception to December 2020. The population of interest included adults who required tracheal intubation for elective surgery under general anesthesia without clear anatomical abnormalities suggesting difficult laryngoscopy. A bivariate model has been used to assess the accuracy of each ultrasound index test to predict difficult direct laryngoscopy.

RESULTS:

Fifteen studies have been considered for quantitative analysis of summary receiver operating characteristic (SROC). The sensitivity for distance from skin to epiglottis (DSE), distance from skin to hyoid bone (DSHB), and distance from skin to vocal cords (DSVC) was 0.82 (0.74–0.87), 0.71 (0.58–0.82), and 0.75 (0.62–0.84), respectively. The specificity for DSE, DSHB, and DSVC was 0.79 (0.70–0.87), 0.71 (0.57–0.82), and 0.72 (0.45–0.89), respectively. The area under the curve (AUC) for DSE, DSHB, DSVC, and ratio between the depth of the pre-epiglottic space and the distance from the epiglottis to the vocal cords (Pre-E/E-VC) was 0.87 (0.84–0.90), 0.77 (0.73–0.81), 0.78 (0.74–0.81), and 0.71 (0.67–0.75), respectively. Patients with difficult direct laryngoscopy have higher DSE, DSVC, and DSHB values than patients with easy laryngoscopy, with a mean difference of 0.38 cm (95% confidence interval [CI], 0.17–0.58 cm; P = .0004), 0.18 cm (95% CI, 0.01–0.35 cm; P = .04), and 0.23 cm (95% CI, 0.08–0.39 cm; P = .004), respectively.

CONCLUSIONS:

Our study demonstrates that airway ultrasound index tests are significantly different between patients with easy versus difficult direct laryngoscopy, and the DSE is the most studied index test in literature to predict difficult direct laryngoscopy. However, it is not currently possible to reach a definitive conclusion. Further studies are needed with better standardization of ultrasound assessment to limit all possible sources of heterogeneity.
Play a Trick and Get a Queen: “Divine Tricksters” in Ancient Korea (and Beyond)
Authors: Riotto Maurizio
Published: December 2021

The issue of trickster in old Korean literature has yet to be discussed in a broadly comparative way in a scientific context. Using a structuralist approach, this article addresses the anthropological theme of the “divine trickster” in some stories from ancient Korea and the ancient West. In particular, by examining three famous episodes from Korean folklore alongside three cases from Western fantastic literature, this article investigates the strategies aimed at acquiring the feminine element as represented by high-ranking foreign women. Starting with the hunting mentality of prehistoric society, where man tries to prevail with intelligence over his prey, the article reviews literary episodes from different anthropological contexts (Indo-European societies, Semitic societies of the Near East, and ancient Korean society), underlining their similarities and differences, but always highlighting and emphasizing the presence of a divine trickster. Ultimately, together with the common denominator of the progressive masculinization of the various societies, we note a more passive role of women in the Korean stories, which appear to be of more recent codification than their Western counterparts, and therefore seem more inspired by cultural patterns of patriarchal orientation.
Turning Songs into Poems and Poems into Songs: Intersections of Literary Sinitic and Vernacular Korean in Chosŏn Literature
Authors: Han Christina
Published: December 2021

This article investigates the dynamic intersections of Literary Sinitic and vernacular Korean and their impact on the innovations in poetry and song in fifteenth- through nineteenth-century Chosŏn Korea. More specifically, it traces the evolution of poetry or song discourse and explores the different strategies employed by Chosŏn poets and songwriters to render oral songs into text. It also investigates the differing views on the function of poetry and song, musical and textual preservation, and emotional and lyrical immediacy, which influenced the composition and translation of song-poems. The article probes the creative collaboration and competition between Literary Sinitic and vernacular Korean, and the fluid relations between translation and vernacularization. On the whole, it explores the ways in which the evolution of poetry-song discourse and the ensuing literary innovations contributed to Chosŏn's complex linguistic ecology.
Avoiding the Radial Paradox: Neuroendovascular Femoral Access Outcomes After Radial Access Adoption
Authors: Wilkinson D. Andrew , Majmundar Neil , Catapano Joshua S. , Cole Tyler S. , Baranoski Jacob F. , Hendricks Benjamin K. , Cavalcanti Daniel D. , Frederickson Vance L. , Ducruet Andrew F. , Albuquerque Felipe C.
Published: December 2021

BACKGROUND:

Transradial access (TRA) for neuroendovascular procedures is increasing in prevalence. The safety benefits of TRA at a patient level may be offset at a population level by a paradoxical increase in transfemoral access (TFA) vascular access site complications (VASCs), the so-called “radial paradox.”

OBJECTIVE:

To study the effect of TRA adoption on TFA performance and outcomes in neuroendovascular procedures.

METHODS:

Data were collected for all procedures performed over a 10-mo period after radial adoption at a single center.

RESULTS:

Over the study period, 1084 procedures were performed, including 719 (66.3%) with an intent to treat by TRA and 365 (33.7%) with an intent to treat by TFA. Thirty-two cases (4.4%) crossed over from TRA to TFA, and 2 cases (0.5%) crossed over from TFA to TRA. TFA was performed in older patients (mean [standard deviation] TFA, 63 [15] vs TRA, 56 [16] years) using larger sheath sizes (≥7 French; TFA, 56.2% vs TRA, 2.3%) (P < .001 for both comparisons). Overall, 29 VASCs occurred (2.7%), including 27 minor (TFA, 4.6% [18/395] vs TRA, 1.3% [9/689], P = .002) and 2 major (TFA, 0.3% [1/395] vs TRA, 0.1% [1/689], P > .99) complications. Independent predictors of VASC included TFA (OR 2.8, 95% confidence interval [CI] 1.1-7.4) and use of dual antiplatelet therapy (OR 4.2, 95% CI 1.6-11.1).

CONCLUSION:

TFA remains an important access route, despite a predominantly radial paradigm, and is disproportionately used in patients at increased risk for VASCs. TFA proficiency may still be achieved in predominantly radial practices without an increase in femoral complications.
The American Society for Stereotactic and Functional Neurosurgery Position Statement on Laser Interstitial Thermal Therapy for the Treatment of Drug-Resistant Epilepsy
Authors: Wu Chengyuan , Schwalb Jason M. , Rosenow Joshua M. , McKhann Guy M. , Neimat Joseph S.
Published: December 2021

Magnetic resonance image–guided laser interstitial thermal therapy (MRgLITT) is a novel tool in the neurosurgical armamentarium for the management of drug-resistant epilepsy. Given the recent introduction of this technology, the American Society for Stereotactic and Functional Neurosurgery (ASSFN), which acts as the joint section representing the field of stereotactic and functional neurosurgery on behalf of the Congress of Neurological Surgeons and the American Association of Neurological Surgeons, provides here the expert consensus opinion on evidence-based best practices for the use and implementation of this treatment modality. Indications for treatment are outlined, consisting of failure to respond to, or intolerance of, at least 2 appropriately chosen medications at appropriate doses for disabling, localization-related epilepsy in the setting of well-defined epileptogenic foci, or critical pathways of seizure propagation accessible by MRgLITT. Applications of MRgLITT in mesial temporal lobe epilepsy and hypothalamic hamartoma, along with its contraindications in the treatment of epilepsy, are discussed based on current evidence. To put this position statement in perspective, we detail the evidence and authority on which this ASSFN position statement is based.
Multiple regions within junctin drive its interaction with calsequestrin-1 and its localization to triads in skeletal muscle
Authors: Rossi Daniela , Lorenzini Stefania , Pierantozzi Enrico , Van Petegem Filip , Osamwonuyi Amadsun David , Sorrentino Vincenzo
Published: December 2021

Junctin is a transmembrane protein of striated muscles, located at the junctional sarcoplasmic reticulum (SR). It is characterized by a luminal C-terminal tail, through which it functionally interacts with calsequestrin and the ryanodine receptor (RyR). Interaction with calsequestrin was ascribed to the presence of stretches of charged amino acids (aa). However, the regions able to bind calsequestrin have not been defined in detail. We report here that, in non-muscle cells, junctin and calsequestrin assemble in long linear regions within the endoplasmic reticulum, mirroring the formation of calsequestrin polymers. In differentiating myotubes, the two proteins colocalize at triads, where they assemble with other proteins of the junctional SR. By performing GST pull-down assays with distinct regions of the junctin tail, we identified two KEKE motifs that can bind calsequestrin. In addition, stretches of charged aa downstream these motifs were found to also bind calsequestrin and the RyR. Deletion of even one of these regions impaired the ability of junctin to localize at the junctional SR, suggesting that interaction with other proteins at this site represents a key element in junctin targeting.
Development of an RNA–protein crosslinker to capture protein interactions with diverse RNA structures in cells
Authors: Han Yan , Guo Xuzhen , Zhang Tiancai , Wang Jiangyun , Ye Keqiong
Published: December 2021

Characterization of RNA–protein interaction is fundamental for understanding the metabolism and function of RNA. UV crosslinking has been widely used to map the targets of RNA-binding proteins, but is limited by low efficiency, requirement for zero-distance contact, and biases for single-stranded RNA structure and certain residues of RNA and protein. Here, we report the development of an RNA–protein crosslinker (AMT–NHS) composed of a psoralen derivative and an N-hydroxysuccinimide ester group, which react with RNA bases and primary amines of protein, respectively. We show that AMT–NHS can penetrate into living yeast cells and crosslink Cbf5 to H/ACA snoRNAs with high specificity. The crosslinker induced different crosslinking patterns than UV and targeted both single- and double-stranded regions of RNA. The crosslinker provides a new tool to capture diverse RNA–protein interactions in cells.
Knowledge and perception of Sepsis among Doctors in Karachi Pakistan
Authors: Ahmed Faiza , Abbasi Lubna , Herekar Fivzia , Jiwani Ahsun , Junaid Patel Muhammad
Published: December 2021

Objectives: To assess knowledge and perception among Pakistani physicians towards sepsis.

Methods: This cross-sectional study was conducted in Indus Hospital and Health Networks from September 2020 to March 2021. The International Sepsis Survey questionnaire was adapted, and its link was sent to trainee physicians as well as specialists, and consultants practicing in various hospitals via social media. Knowledge and perception were scored and 50% was considered the cut-off score for adequacy. Data was analyzed using SPSS version 26.

Results: Analysis was done on 222 respondents who completed the survey. 37.9% of the participants had adequate knowledge. Knowledge regarding sepsis was significantly associated with specialty, ICU/CCU/HDU, and work experience (P-value <0.0001). More recent trainee physicians and those with more experience in critical care areas demonstrated better knowledge. Over 2/3rd of the respondents strongly agreed that sepsis remains one of the unmet needs in critical care today.

Conclusion: A common belief exists that sepsis remains a challenge to treat among doctors. Moreover, there is consensus that it is the most frequently miss diagnosed condition in critical care and a dire need exists for its early diagnosis. Additionally, prompt management of presumed sepsis is imperative to improve outcomes.

doi: https://doi.org/10.12669/pjms.38.ICON-2022.5775

How to cite this:Ahmed F, Abbasi L, Herekar F, Jiwani A, Patel MJ. Knowledge and perception of Sepsis among Doctors in Karachi Pakistan. Pak J Med Sci. 2022;38(2):380-386. doi: https://doi.org/10.12669/pjms.38.ICON-2022.5775

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Voice against tobacco: A call for integrated action for effective change
Authors: Saeed Saima , Shahroz Inayat Muhammad , Khan Suniya Umar , Agha Alina Ally
Published: December 2021

doi: https://doi.org/10.12669/pjms.38.ICON-2022.5788

How to cite this:Saeed S, Shahroz IM, Khan SU, Agha AA. Voice against tobacco: A call for integrated action for effective change. Pak J Med Sci. 2022;38(2):436-437.  doi: https://doi.org/10.12669/pjms.38.ICON-2022.5788
An ecological study on the association between early childhood caries and intimate partner violence in 20 low- and middle-income countries: 2007-2017
Authors: Folayan Morenike Oluwatoyin , Obiyan Mary O. , El Tantawi Maha , Kemoli Arthur , Al-Batayneh Ola B. , Gaffar Balgis , Schroth Robert J. ,   Early Childhood Caries Advocacy Group
Published: December 2021

Background:Women are the worst affected by intimate partner violence (IPV), and this impacts negatively on the health of the children they care for. This study aimed to determine the relationship between IPV and the prevalence of early childhood caries (ECC) in 3-5-year-olds.

Methods:This was an ecological study using IPV (physical, sexual, emotional) data extracted from the Demographic Health Survey of 20 low- and middle-income countries and ECC data for 3-5-year-olds of the same countries for the period 2007-2017. Linear regression analysis was used to assess the relationship between the percentage of 3-5-year-olds with ECC (outcome variable) and IPV indicators (physical, sexual, emotional). The model was adjusted for the country’s gross national income and the percentage of women with secondary or higher education. Partial eta squared (ηp2), regression coefficients, confidence intervals and p-values were calculated.

Results:Data on ECC in 3-5-year-olds and IPV were available for six low-income-countries, 10 lower-middle-income-countries and four upper-middle-income-countries. The most prevalent form of IPV was physical violence (10.09%). The Democratic Republic of Congo had the highest prevalence of physical violence (45.8%), sexual violence (25.4%), and ECC (80.0%). The strongest association was between the prevalence of ECC and emotional violence (ηp2=0.01), followed by physical violence (ηp2=0.005), and sexual violence (ηp2=0.003). For every 1% higher prevalence of emotional violence, there was 0.28% higher prevalence of ECC, and for every 1% higher percentage of physical violence, there was 0.21% higher prevalence of ECC. On the contrary, for every 1% higher prevalence of sexual violence, there was 0.35% lower prevalence of ECC prevalence.

Conclusions:The association between IPV and the prevalence of ECC in 3-5-year-olds is minor, with the strongest direct association effect being with emotional violence; and there was an inverse association between sexual violence and the prevalence of ECC. These findings need to be studied further.
Student teachers' perceptions of the collaborative relationships form between universities and inclusive elementary schools in Indonesia
Authors: Rasmitadila Rasmitadila , Humaira Megan Asri , Rachmadtullah Reza
Published: December 2021

Background: The collaborative relationship between universities and inclusive elementary schools has not been maximally practiced. The form of collaboration that universities with inclusive elementary schools have carried out is still limited to the need to complete lecture materials in the semester. There is a gap between the theory and practice obtained by student teachers at universities when they have to teach in inclusive elementary schools. As a result, they have not contributed to solving problems that occur in inclusive elementary schools. The collaborative relationship between inclusive elementary schools and universities directly implies that the success of inclusive education is determined by the competence of student teachers whose universities have successfully educated them in order to teach in inclusive elementary schools. Against the background that the inclusive education system is developing in Indonesia, the researchers investigated student teachers' perceptions at universities about inclusive university-inclusive elementary school collaborative relationships.

Methods: During data collection, an online survey and in-depth interviews of student teachers about individual experiences and their ideas about the form of inclusive elementary schools-university partnerships was conducted. The data analysis used is a thematic analysis technique.

Result: The result summarizes student teachers' statements, revealed three main themes: provision of inclusive education needs, research, and field practice. The student teachers revealed that the collaborative relationship between universities and inclusive elementary schools is essential to develop holistic, inclusive practices in a collaborative partnership based on input-needs, which has a two-way impact or benefit for both parties.

Conclusions: Furthermore, collaborative relationships must be in the form of long-term programs, such as continuous assistance, and adaptation to the development of inclusive education through lecture materials. To achieve inclusive education in Indonesia, we also recommend that the government make policies on multi-sectoral collaboration in order to support inclusive education.