bluuebunny/crossref_metadata_2025_split huggingface dataset:
Zymomonas mobilis as an emerging biotechnological chassis for the production of industrially relevant compounds
Authors: Braga Adelaide , Gomes Daniela , Rainha João , Amorim Cláudia , Cardoso Beatriz B. , Gudiña Eduardo J. , Silvério Sara C. , Rodrigues Joana L. , Rodrigues Lígia R. 
Published: December 2021

AbstractZymomonas mobilis is a well-recognized ethanologenic bacterium with outstanding characteristics which make it a promising platform for the biotechnological production of relevant building blocks and fine chemicals compounds. In the last years, research has been focused on the physiological, genetic, and metabolic engineering strategies aiming at expanding Z. mobilis ability to metabolize lignocellulosic substrates toward biofuel production. With the expansion of the Z. mobilis molecular and computational modeling toolbox, the potential of this bacterium as a cell factory has been thoroughly explored. The number of genomic, transcriptomic, proteomic, and fluxomic data that is becoming available for this bacterium has increased. For this reason, in the forthcoming years, systems biology is expected to continue driving the improvement of Z. mobilis for current and emergent biotechnological applications. While the existing molecular toolbox allowed the creation of stable Z. mobilis strains with improved traits for pinpointed biotechnological applications, the development of new and more flexible tools is crucial to boost the engineering capabilities of this bacterium. Novel genetic toolkits based on the CRISPR-Cas9 system and recombineering have been recently used for the metabolic engineering of Z. mobilis. However, they are mostly at the proof-of-concept stage and need to be further improved.
Graphical Abstract
Duodenal stenosis associated with an ectopic opening of the common bile duct into the duodenal bulb: a case report
Authors: Kobayashi Kazuki , Murayama Michinori , Sugasawa Hidekazu , Nishikawa Makoto , Nishiyama Kiyoshi , Takeo Hiroaki 
Published: December 2021

Abstract
Background
Ectopic opening of the common bile duct is a rare congenital biliary anomaly. Herein, we present a case of duodenal stenosis with ectopic opening of the common bile duct into the duodenal bulb.

Case presentation
A 54-year-old man was referred with fever, nausea, and vomiting. He had experienced epigastric pain several times over the past 30 years. Endoscopy showed a post-bulbar ulcer, a submucosal tumor of the duodenum, and a small opening with bile secretion. Contrast duodenography revealed duodenal stenosis and bile reflux with a common bile duct deformity. Pancreatoduodenectomy was performed because of the clinical suspicion of a biliary neoplasm or groove pancreatitis. The resected specimen showed an ectopic opening of the common bile duct into the duodenal bulb and no tumor.

Conclusions
Ectopic opening of the common bile duct into the duodenal bulb is complicated by a duodenal ulcer, deformity, and stenosis mimicking groove pancreatitis or pancreatic tumors. Although rare, we should be aware of this anomaly for an accurate diagnosis.
Clinical Oncology Workload in Sri Lanka: Infrastructure, Supports, and Delivery of Clinical Care
Authors: Gunasekera Sanjeeva , Seneviratne Sanjeewa , Jalink Matthew , Joseph Nuradh , Ariyarathna Yasantha , Booth Christopher M. , Wijeratne Don Thiwanka 
Published: December 2021

PURPOSESri Lanka is a lower middle-income country undergoing a demographic transition with an increasing aging population. This has given rise to a higher burden of noncommunicable diseases including cancer. A well-trained oncology workforce is essential to address this growing public health challenge. Understanding the baseline status of the clinical oncology workforce is an essential step to improving cancer care delivery in Sri Lanka.METHODSIn this cross-sectional study, we distributed a web-based survey to all clinical oncologists in Sri Lanka. The survey captured data regarding clinical workload, demographic details, practice setting, and perceived barriers to quality patient care.RESULTSA total of 41 of 54 oncologists responded to the survey, and all participants had training in clinical oncology. Thirty-seven (90%) of 41 oncologists treated both solid and hematologic malignancies, and the median duration of independent practice was 5 years. Almost two thirds of the oncologists (26 of 41, 63%) work at an academic center, and two thirds of the oncologists (27 of 41, 66%) work in both public and private sectors. A majority of the oncologists (26 of 41, 63%) were on-call 7 days per week. More than half of the oncologists saw over 400 new patient consults per year. With regard to barriers to quality patient care, most of the concerns relate to the scarcity of resources.CONCLUSIONThis study sheds significant light about the clinical oncology workload landscape in Sri Lanka. Compared with other low- and middle-income countries, Sri Lankan clinical oncologists are faced with a very high workload, which may affect delivery or care.
Positive Association Between Location of Melanoma, Ultraviolet Signature, Tumor Mutational Burden, and Response to Anti–PD-1 Therapy
Authors: Dousset Léa , Poizeau Florence , Robert Caroline , Mansard Sandrine , Mortier Laurent , Caumont Charline , Routier Émilie , Dupuy Alain , Rouanet Jacques , Battistella Maxime , Greliak Anna , Cappellen David , Galibert Marie-Dominique , Allayous Clara , Lespagnol Alexandra , Gerard Émilie , Kerneuzet Inès , Roy Séverine , Dutriaux Caroline , Merlio Jean-Philippe , Vergier Beatrice , Schrock Alexa B. , Lee Jessica , Ali Siraj M. , Kammerer-Jacquet Solène-Florence , Lebbé Céleste , Beylot-Barry Marie , Boussemart Lise 
Published: December 2021

PURPOSEEmerging evidence suggests a correlation between the tumor mutational burden (TMB) and the response to programmed cell death-1 protein (PD-1) monotherapy across multiple cancer types. In skin cancers, as high TMB is mostly because of ultraviolet (UV) exposure, we hypothesized a correlation between the primary melanoma cutaneous location according to sun exposure and response to anti–PD-1 monotherapy.METHODSThe aim of this study was to analyze, in advanced melanoma, the relationship between TMB, locations according to sun exposure, and response to PD-1 inhibitors. We conducted a prospective multicentric analysis, by sequencing the most recent metastatic sample before PD-1 inhibitors using FoundationOne assay.RESULTSOne hundred two patients were included, with TMB available for 94 cases. In univariate and multivariate linear regression, TMB was significantly associated with sun-exposed areas of the primary melanoma location and with age (coefficients of the association with log-TMB: non-UV location, –1.05; chronic sun-exposed area, 1.12; P value for the location, < 10–5; age, 0.021 per year, P value for age, .002). Molecular UV signature present on the metastatic site was associated with higher TMB ( P = .003). Melanomas bearing a high TMB had a higher probability of response to PD-1 inhibitors compared with melanomas with a low TMB, with a dose-dependent effect following an exponential curve and a negative odds ratio of 0.40 (95% CI, 0.20 to 0.72, P = .004) between log-TMB and 6-month progression.CONCLUSIONCumulative sun exposure related to skin location and molecular UV signature present on the metastatic site appear to be relevant biomarkers directly linked to TMB. Because TMB is not yet available to all for routine clinical use, the location of the primary melanoma in a sun-exposed area may play an important role in clinical decisions regarding therapeutic choice.
Procedure-Related Outcomes Including Readmission Following Spinal Cord Stimulator Implant Procedures: A Retrospective Cohort Study
Authors: Goel Vasudha , Kumar Varun , Patwardhan Amol M. , Ibrahim Mohab , Sivanesan Eellan , Darrow David , Shankar Hariharan 
Published: December 2021

BACKGROUND:
Spinal cord stimulation (SCS) has been shown to reduce opioid consumption, reduce pain, improve quality of life compared to conventional therapy, and be more effective than spine reoperation in carefully selected patients. In this study, we evaluate readmissions after SCS implantation procedures, costs, predictors, and etiologies for readmission following implantation procedures.

METHODS:
The study was a retrospective cohort using the National Readmissions Database from 2013 to 2017. Administrative billing codes were used to identify patients undergoing SCS implantation procedures. The primary outcome of our study was 30-day readmission following the SCS implantation procedure. Continuous outcomes were compared between groups using the Student t test or Wilcoxon rank sum test. In addition, multivariable predictors of 30-day readmission were assessed by hierarchical logistic regression analysis.

RESULTS:
A total of 3737 (26.7% open surgical SCS implants [OS-SCS]) individuals admitted to the hospital for SCS implantation were included in the final cohort analysis. The cohort consisted of predominantly female patients (58.71%) and in the 50- to 64-year age group (35.46%). Patients who underwent open surgical SCS implantation had a longer length of stay during the initial admission and a higher 30-day readmission rate (9.4% vs 7% P = .01). OS-SCS, older age, lower socioeconomic status, patients with specific comorbidities (ie, hypertension or chronic obstructive pulmonary disease [COPD]), and home discharge are associated with readmission.

CONCLUSIONS:
Readmission rates after SCS implantation are around 7.7% in the United States. Infection and postoperative complications remain the top etiologies for readmission. Open surgical SCS implantation is associated with more extended initial hospitalization and a higher rate of readmission when compared to percutaneous SCS implantation procedures.
The zebrafish issue: 25 years on
Authors: Mullins Mary C. , Acedo Joaquín Navajas , Priya Rashmi , Solnica-Krezel Lilianna , Wilson Stephen W. 
Published: December 2021

ABSTRACT
In the 1990s, labs on both sides of the Atlantic performed the largest genetic mutagenesis screen at that time using an emerging model organism: the zebrafish. Led by Christiane Nüsslein-Volhard in Tübingen, Germany, and Wolfgang Driever in Boston, USA, these colossal screens culminated in 1996 with the publication of 37 articles in a special issue of Development, which remains the journal's largest issue to this day. To celebrate the anniversary of the zebrafish issue and reflect on the 25 years since its publication, five zebrafish researchers share what the issue means to them, how it has contributed to their career and its impact on the zebrafish community.
Novel preclinical model for CDKL5 deficiency disorder
Authors: Serrano Rita J. , Lee Clara , Douek Alon M. , Kaslin Jan , Bryson-Richardson Robert J. , Sztal Tamar E. 
Published: December 2021

ABSTRACT
Cyclin-dependent kinase-like-5 (CDKL5) deficiency disorder (CDD) is a severe X-linked neurodegenerative disease characterised by early-onset epileptic seizures, low muscle tone, progressive intellectual disability and severe motor function. CDD affects ∼1 in 60,000 live births, with many patients experiencing a reduced quality of life due to the severity of their neurological symptoms and functional impairment. There are no effective therapies for CDD, with current treatments focusing on improving symptoms rather than addressing the underlying causes of the disorder. Zebrafish offer many unique advantages for high-throughput preclinical evaluation of potential therapies for neurological diseases, including CDD. In particular, the large number of offspring produced, together with the possibilities for in vivo imaging and genetic manipulation, allows for the detailed assessment of disease pathogenesis and therapeutic discovery. We have characterised a loss-of-function zebrafish model for CDD, containing a nonsense mutation in cdkl5. cdkl5 mutant zebrafish display defects in neuronal patterning, seizures, microcephaly, and reduced muscle function caused by impaired muscle innervation. This study provides a powerful vertebrate model for investigating CDD disease pathophysiology and allowing high-throughput screening for effective therapies.
This article has an associated First Person interview with the first author of the paper.
Combining Non-invasive Ventilation with timed position change in the Emergency Department to improve oxygenation and outcomes in patients with COVID-19: A prospective analysis from a low resource setup
Authors: Ali Saima , Khatri Adeel , Ghouri Nida , Mukhtar Sama , Zawawi Suha , Saleem Syed Ghazanfar 
Published: December 2021

Background: Moving away from invasive ventilation towards timed position change and non-invasive ventilation is especially of benefit in low and middle income countries, where judicious use of the available healthcare resources is the need of the day. Our study was conducted prospectively to develop strategies for non-invasive ventilation in combination with timed position change of patients to see its impact on their outcome.Objectives: Non-invasive ventilation has proven to be of benefit in COVID-19 related acute lung injury. The objective of this prospective, cross sectional study was to develop a protocol for the use of non-invasive ventilation with timed position change to improve COVID-19 patients’ outcomes in the Emergency Department (ED).
Methods: All patients presenting with confirmed or suspected COVID-19 were enrolled in the study from March 2020 to October 2020. Data was collected to see the effect of timed position change and non-invasive ventilation on these patients and its effect on delaying or avoiding invasive ventilation.
Results: Of the 207 COVID-19 patients presenting to the IHHN ED, 109(52.7%) had oxygen saturation in the nineties in supine position followed by right lateral in 37(17.9%), sitting up in 30(14.5%), left lateral in 29(14%) and prone position in 2(1%). Maximal oxygenation was achieved with non rebreather mask (NRM) and nasal prongs in 87(42%) of the patients, followed by the use of continuous positive airway pressure (CPAP) in 29(14%).
Conclusion: Most of the patients preferred to stay in the supine position and described it as the position of comfort. When used in combination supine position, patients on NRM with nasal prongs and on CPAP, had oxygen saturation in the nineties. Central obesity was found to be the prime reason for the inability to prone our patients. This needs to be followed up in the current fourth wave of COVID-19 to see the effectiveness of the said modalities.
doi: https://doi.org/10.12669/pjms.38.ICON-2022.5772
How to cite this:Ali S, Khatri A, Ghouri N, Mukhtar S, Zawawi S, Saleem SG. Combining Non-invasive Ventilation with timed position change in the Emergency Department to improve oxygenation and outcomes in patients with COVID-19: A prospective analysis from a low resource setup. Pak J Med Sci. 2022;38(2):375-379. doi: https://doi.org/10.12669/pjms.38.ICON-2022.5772
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.
The Obstructive Lung Diseases Program: Integrated obstructive lung disease services within primary care in Pakistan
Authors: Saeed Saima , Siddiqui Madiha , Altaf Rahma 
Published: December 2021

Objective: To assess the learning impact of e-curriculums on healthcare professionals (HCPs). The second objective was to report the screening, detection and clinical features of patients with obstructive lung diseases (OLD) through an integrated care program at The Indus Hospital & Health Network (IHHN), Karachi, Pakistan.
Methods: A retrospective, observational study was conducted in the Family Medicine outpatient department from January 2019 till July 2021. HCPs were trained on the diagnosis and management of OLD through e-learning. Patients were screened clinically for OLD and had spirometry performed if suspect. Baseline characteristics, patient-reported outcome measures (PROMs), spirometry and treatment modalities were collected. Univariate analysis was done on Excel and paired t-testing was performed on Stata 16.
Results: Online training on clinical aspects of OLD was completed by 33 HCPs, amongst whom 77.9% demonstrated improved post-test evaluations of 26.8% (p=0.000). Of 1896 patients screened, 60.8% were diagnosed as OLD. Asthmatics accounted for 66.5% (60.9% females, median age 39 years). In 84.5% of patients who completed PROMs, poor control of symptoms was reported. Inhaler technique was taught in 66.5%. Breathless patients, with a high modified Medical Research Council score (mMRC ≥ 2, n=234), were referred for pulmonary rehabilitation in 92% of cases. Tobacco cessation advice was delivered to 61.1% of all current users (n=229).
Conclusion: The OLD program uses capacity building, gold standard diagnostics and updated management strategies in primary care, allowing earlier diagnosis of suspected patients and implementation of evidence-based interventions, aiming to improve their morbidity and mortality.
doi: https://doi.org/10.12669/pjms.38.ICON-2022.5781
How to cite this:Saeed S, Siddiqui M, Altaf R. The Obstructive Lung Diseases Program: Integrated obstructive lung disease services within primary care in Pakistan. Pak J Med Sci. 2022;38(2):334-339. doi: https://doi.org/10.12669/pjms.38.ICON-2022.5781
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.
To determine the association between asthma severity and hospital admission measured by Pediatric Respiratory Assessment Measure (PRAM) score at Indus Hospital and Health Network, Karachi, Pakistan, 2020-2021
Authors: Kazi Unaisa , Gul Rukh Saira , Zawawi Suha , Laila Saba , Fareeduddin Mohammad , Saleem Syed Ghazanfar 
Published: December 2021

Objectives: To determine the association between asthma severity and the likelihood of hospitalization by using Pediatric Respiratory Assessment Measure (PRAM) score for pediatric patients who present to the emergency department (ED) with mild, moderate or severe asthma exacerbations and those who received standard intensive asthma therapy.
Methods: This was a retrospective study conducted in children aged between 2 to 14 years. The data was entered and analysed using Statistical Package for the Social Sciences (SPSS) version 21. To be included in the study, the children must have received “intensive asthma therapy” defined as administration of systemic corticosteroids with three albuterol treatments and ipratropium.
Results: A total of 437 patients were enrolled in the study out of which 250 were male and 187 were female. The mean age was 6.1 ± 3.4 years with a minimum age of two and a maximum age of 14 years. The 4-hour PRAM score (AUC = 0.88) overall significantly improved the predictive value of admission (p value <0.001) as compared to the PRAM score calculated at triage (AUC = 0.81).
Conclusion: The 4-hour PRAM score is the best predictor for the need of hospitalization. It is suggested that these results are applied clinically in the pediatric ED to improve patient flow and to better facilitate intensive therapy of patients at triage to decrease the need for hospitalization.
doi: https://doi.org/10.12669/pjms.38.ICON-2022.5783
How to cite this:Kazi U, Gul Rukh S, Zawawi S, Laila S, Fareeduddin M, Saleem SG. To determine the association between asthma severity and hospital admission measured by Pediatric Respiratory Assessment Measure (PRAM) score at Indus Hospital and Health Network, Karachi, Pakistan, 2020-2021. Pak J Med Sci. 2022;38(2):345-350. doi: https://doi.org/10.12669/pjms.38.ICON-2022.5783
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.
An outbreak of Salmonella Enteritidis food poisoning following consumption of chicken shawarma: A brief epidemiological investigation
Authors: Deepanjali Surendran , Jharna Mandal , Chanaveerappa Bammigatti , Sarumathi Dhandapani , Gopichand Pallam , Anupriya Kaliyappan 
Published: December 2021

Background: Shawarma, a popular meat-based fast food could be a source of foodborne outbreak due to non-typhoidal Salmonella (NTS). A clustering of acute gastrointestinal (GI) illness following intake of chicken shawarma occurred primarily among the staff and students of a tertiary care hospital in southern India. Methods: A case-control study was conducted among 348 undergraduate medical students (33 cases, 315 controls). Data was collected using direct interviews and a simple online questionnaire. Epidemiological associations of GI illness were evaluated at three levels of exposure namely-eating food from any restaurant, eating food from the implicated food outlet, eating chicken shawarma from the implicated outlet. Results: Of 33 cases, 26 had consumed food from a particular food outlet, 4 from other outlets, and 3 did not report eating out. Consumption of food from the suspected food outlet was significantly associated with GI illness (odds ratio 121.8 [95% CI 28.41 to 522.66]; P<0.001); all the 26 cases who had eaten from the particular outlet had eaten chicken shawarma. By comparison, only one of the 315 controls had eaten this dish. Of the 27 persons (cases as well as controls) who had consumed chicken shawarma from the outlet, 26 were ill. Culture of stool samples from 10 affected individuals and implicated food item yielded Salmonella Enteritidis. Conclusions: Meat-based shawarma is a potential source of NTS infection. Food safety authorities should enforce guidelines for safe preparation and sale of shawarmas and similar products.
A narrative inquiry into the resettlement of armed forces personnel in the Arabian Gulf: a model for successful transition and positive mental well-being
Authors: Mottershead Richard , Alonaizi Nafi 
Published: December 2021

Background: The study sought to explore the lived experiences of individuals having served in the Armed Forces of Saudi Arabia, as they made the transition to civilian life and sought new employment opportunities. Methods: Researchers carried out qualitative research in the form of narrative inquiry. Narratives were collected from eleven in-depth interviews conducted in Saudi Arabia in 2021, allowed for insight into participant experiences. Existing literature on military retirement was also investigated. Results: Interviews were transcribed verbatim and analyzed concurrently using thematic analysis to identify patterns or themes. The researchers adopted thematic synthesis as an analytical framework though which descriptive themes from the literature on military retirement were generated. Overall, this approach allowed for the comparison of themes in literature with those of narrative interviews. Conclusion: The study identified challenges encountered by veterans during the resettlement and transitional phase from military to civilian life. There was a general consensus, however, that military life equips individuals with valuable skills that are transferrable to successful post-military employment, known as Positive Transferable Adaptability for Employability (PTAE), (Mottershead, 2019), which can greatly empower those making the transition. These findings led the researchers to develop a new model for veteran career paths that meet the contemporary employment needs of the Kingdom of Saudi Arabia: the REVERE Transition Model, which identifies six career paths.