bluuebunny/crossref_metadata_2025_split huggingface dataset:
Real-time forecasting the trajectory of monkeypox outbreaks at the national and global levels, July – October 2022
Authors: Bleichrodt Amanda , Dahal Sushma , Maloney Kevin , Casanova Lisa , Luo Ruiyan , Chowell Gerardo 
Published: November 2022

AbstractBackgroundBeginning May 7, 2022, multiple nations reported an unprecedented surge in monkeypox cases. Unlike past outbreaks, differences in affected populations, transmission mode, and clinical characteristics have been noted. With the existing uncertainties of the outbreak, real-time short-term forecasting can guide and evaluate the effectiveness of public health measures.MethodsWe obtained publicly available data on confirmed weekly cases of monkeypox at the global level and for seven countries (with the highest burden of disease at the time this study was initiated) from the Our World in Data (OWID) GitHub repository and CDC website. We generated short-term forecasts of new cases of monkeypox across the study areas using an ensemble n-sub-epidemic modeling framework based on weekly cases using 10-week calibration periods. We report and assess the weekly forecasts with quantified uncertainty from the top-ranked, second-ranked, and ensemble sub-epidemic models. Overall, we conducted 324 weekly sequential 4-week ahead forecasts across the models from the week of July 28th, 2022, to the week of October 13th, 2022.ResultsThe last 10 of 12 forecasting periods (starting the week of August 11th, 2022), show either a plateauing or declining trend of monkeypox cases for all models and areas of study. According to our latest 4-week ahead forecast from the top-ranked model, a total of 6232 (95% PI: 487.8, 12468.0) cases could be added globally from the week of 10/20/2022 to the week of 11/10/2022. At the country level, the top-ranked model predicts that the United States will report the highest cumulative number of new cases for the 4-week forecasts (median based on OWID data: 1806 (95% PI: 0.0, 5544.5)). The top-ranked and weighted ensemble models outperformed all other models in short-term forecasts.ConclusionsOur top-ranked model consistently predicted a decreasing trend in monkeypox cases on the global and country-specific scale during the last ten sequential forecasting periods. Our findings reflect the potential impact of increased immunity, and behavioral modification among high-risk populations.
Prevalence of cirrhotic cardiomyopathy according to different diagnostic criteria. Alterations in ultrasonographic parameters of both left and right ventricles before and after stress
Authors: Karagiannakis Dimitrios S , Stefanaki Katerina , Anastasiadis George , Voulgaris Theodoros , Vlachogiannakos Jiannis 
Published: November 2022

AbstractBackgroundPrevalence of cirrhotic cardiomyopathy (CC) remains controversial. Several guidelines have been proposed for its assessment.AimTo estimate the frequency of CC by using all of the proposed diagnostic criteria, to describe the whole spectrum of cardiac alterations and investigate the role of stress in unmasking latent cases of CC.MethodsNinety consecutive patients were recruited. CC was evaluated by using the Montreal, the 2009 and 2019 criteria. Dobutamine stress test was also performed.ResultsLVDD was identified in 72(80%), 36(40%) and 10(11.1%) patients based on the above criteria, respectively. None of the patients had right ventricular systolic dysfunction, neither at rest, nor after stress. Stress test revealed left systolic dysfunction in 4(4.5%) patients. According to 2019 criteria, presence of LVDD was not associated with gender, etiology, or staging of liver disease. Patients with LVDD had longer QTc (p=0.002), larger LAvol (p=0.0001), lower TAPSE(s) (p=0.012), lower SRV(s) (p=0.0001) and lower ΔCI (p=0.009) compared to those without. Patients with Child-B/C had longer QTc (p=0.004), higher BNP (p=0.016), higher E/e’ (p=0.0001) and higher E/e’(s) (p=0.003), compared to Child-A patients. A significant correlation was demonstrated between Child-Pugh score and E/e’ (p=0.0001), or E/e’(s) (p=0.002).ConclusionsIn accordance with the recent guidelines the prevalence of CC seems to be lower. LVDD is the predominant feature of CC and aggravates along with the severity of liver disease. After dobutamine administration several sonographic variables exacerbate, particularly in Child-B/C patients, indicating a potential higher risk for clinical heart failure during stressful invasive interventions.
Modeling post-holiday surge in COVID-19 cases in Pennsylvania counties
Authors: Ren Benny , Hwang Wei-Ting 
Published: November 2022

AbstractCOVID-19 arrived in the United States in early 2020, with cases quickly being reported in many states including Pennsylvania. Many statistical models have been proposed to understand the trends of the COVID-19 pandemic and factors associated with increasing cases. While Poisson regression is a natural choice to model case counts, this approach fails to account for correlation due to spatial locations. Being a contagious disease and often spreading through community infections, the number of COVID-19 cases are inevitably spatially correlated as locations neighboring counties with a high COVID-19 case count are more likely to have a high case count. In this analysis, we combine generalized estimating equations for Poisson regression, a popular method for analyzing correlated data, with a semivariogram, to model daily COVID-19 case counts in 67 Pennsylvania counties between March 20, 2020 to January 23, 2021 in order to study infection dynamics during the beginning of the pandemic. We use a semivariogram that describes the spatial correlation as a function of the distance between two counties as the working correlation. We further incorporate a zero-inflated model in our spatial GEE to accommodate excess zeros in reported cases due to logistical challenges associated with disease monitoring. By modeling time-varying holiday covariates, we estimated the effect of holiday timing on case count. Our analysis showed that the incidence rate ratio was significantly greater than one, 6-8 days after a holiday suggesting a surge in COVID-19 cases approximately one week after a holiday.
Vitamin D supplementation improves the prognosis of patients with colorectal cancer liver metastases
Authors: Rada Miran , Krzywon Lucyna , Kapelanski-Lamoureux Audrey , Kim Diane , Petrillo Stephanie , Lazaris Anthoula , Metrakos Peter 
Published: November 2022

AbstractColorectal cancer liver metastasis (CRCLM) is one of the deadliest cancers. CRCLM tumours have two distinct histopathological growth patterns (HGPs) including desmoplastic HGP (DHGP) and replacement HGP (RHGP). The DHGP tumours are angiogenic, while their RHGP counterparts are vessel co-opting. The patients with DHGP tumours have a better response to anti-angiogenic agents and chemotherapy, as well as the prognosis. To determine the influence of vitamin D supplementation in CRCLM, we analyzed the HGPs and the 5-year OS of CRCLM patients (n=106). Interestingly, we found an inverse correlation between vitamin D supplementation and the presence of RHGP tumours in CRCLM patients. Additionally, the 5-year OS of the patients that administered vitamin D was significantly higher. The cancer cells in RHGP lesions are characterized by direct contact with the hepatocytes, and this phenomenon enhances the motility of the cancer cells and facilitates their infiltration through liver parenchyma to co-opt the pre-existing vessels. Significantly, our in vitro data demonstrated the downregulation of motility markers in the co-cultured cancer cells with hepatocytes upon exposure to vitamin D. Altogether, this study highlights the role of vitamin D in CRCLM and provides a rationale to investigate the contribution of vitamin D supplementation to the prognosis of CRCLM patients.
Morning Report Improves Residents’ Diagnostic Competence & Clinical Problem-Solving Ability
Authors: Tariq Muhammad , Vaqar Maham , Abid Shahab , Jafri Wasim 
Published: November 2022

ABSTRACTIntroductionMorning report (MR) is an educational activity that uses inpatient case-based teaching. Given the rapid changes taking place in medical practice, it is important to assess the residents’ perspective regarding this teaching method.ObjectiveTo establish the perspective of residents in internal medicine on various aspects of MR and propose a format based on our observations.Study DesignObservational cross-sectional study.Place & Duration of StudyData was collected from groups of residents in the Department of Medicine at the Aga Khan University Hospital, from July 2002 to August 2007.MethodologyAn observational cross-sectional survey on MR was conducted among the residents of the Department of Medicine at Aga Khan University. A 22-item questionnaire was distributed among the residents based on the purpose, format, and contents of the morning report, as well as the most appropriate person to present and conduct it, and how frequently they should be carried out.Analyses were carried out using the statistical software ‘Statistical Package for Social Sciences’ (SPSS)Results92% of residents believed MR to be an effective teaching activity with 65% of them choosing ‘Improvement in clinical problem-solving ability’ as the primary purpose of MR followed by ‘improving presentation skills’ (62%) and ‘conveying medical knowledge to the residents’ (58%). 79 residents (87%) believed that the junior resident should present the case history. 75 residents (83%) thought that faculty on call at time of patient’s admission should conduct MR. Residents wanted to discuss diagnostic work-up (90%) and management (89%) of specific interesting cases (79%) in MR.ConclusionMR is an effective educational activity and should be an essential component of any post-graduate residency program within the country and outside.
Nirmatrelvir and the Risk of Post-Acute Sequelae of COVID-19
Authors: Xie Yan , Choi Taeyoung , Al-Aly Ziyad 
Published: November 2022

AbstractLong Covid – the disease encompassing the post-acute sequelae of SARS-CoV-2 (PASC) —affects millions of people around the world. Prevention of PASC is an urgent public health priority. In this work, we aimed to examine whether treatment with nirmatrelvir in the acute phase of COVID-19 is associated with reduced risk of post-acute sequelae. We used the healthcare databases of the US Department of Veterans Affairs to identify users of the health system who had a SARS-CoV-2 positive test between March 01, 2022 and June 30, 2022, were not hospitalized on the day of the positive test, had at least 1 risk factor for progression to severe COVID-19 illness and survived the first 30 days after SARS-CoV-2 diagnosis. We identify those who were treated with oral nirmatrelvir within 5 days after the positive test (n=9217) and those who received no COVID-19 antiviral or antibody treatment during the acute phase of SARS-CoV-2 infection (control group, n= 47,123). Inverse probability weighted survival models were used to estimate the effect of nirmatrelvir (versus control) on a prespecified panel of 12 post-acute COVID-19 outcomes and reported as hazard ratio (HR) and absolute risk reduction (ARR) in percentage at 90 days. Compared to the control group, treatment with nirmatrelvir was associated with reduced risk of PASC (HR 0.74 95% CI (0.69, 0.81), ARR 2.32 (1.73, 2.91)) including reduced risk of 10 of 12 post-acute sequelae in the cardiovascular system (dysrhythmia and ischemic heart disease), coagulation and hematologic disorders (deep vein thrombosis, and pulmonary embolism), fatigue, liver disease, acute kidney disease, muscle pain, neurocognitive impairment, and shortness of breath. Nirmatrelvir was also associated with reduced risk of post-acute death (HR 0.52 (0.35, 0.77), ARR 0.28 (0.14, 0.41)), and post-acute hospitalization (HR 0.70 (0.61, 0.80), ARR 1.09 (0.72, 1.46)). Nirmatrelvir was associated with reduced risk of PASC in people who were unvaccinated, vaccinated, and boosted, and in people with primary SARS-CoV-2 infection and reinfection. In sum, our results show that in people with SARS-CoV-2 infection who had at least 1 risk factor for progression to severe COVID-19 illness, treatment with nirmatrelvir within 5 days of a positive SARS-CoV-2 test was associated with reduced risk of PASC regardless of vaccination status and history of prior infection. The totality of findings suggests that treatment with nirmatrelvir during the acute phase of COVID-19 reduces the risk of post-acute adverse health outcomes.
Rapid Acquisition and Transmission of Drug Resistance Amongst Beijing LineageMycobacterium tuberculosisin Vietnam
Authors: Silcocks Matthew , Chang Xuling , Thuong Thuong Nguyen Thuy , Qin Youwen , Minh Ha Dang Thi , Khac Thai Phan Vuong , Vijay Srinivasan , Anh Thu Do Dang , Nhung Hoang Ngoc , Lan Nguyen Huu , Quynh Nhu Nguyen Thi , Edwards David , Nath Artika , Pham Kym , Bang Nguyen Duc , Hong Chau Tran Thi , Thwaites Guy , Heemskerk A. Dorothee , Khor Chiea Chuen , Teo Yik Ying , Inouye Michael , Ong Rick Twee-Hee , Caws Maxine , Holt Kathryn E. , Dunstan Sarah J. 
Published: November 2022

AbstractWhole genome sequencing (WGS) and phenotypic drug susceptibility testing was performed on a collection of 2,542Mycobacterium tuberculosis (Mtb)isolates from tuberculosis (TB) patients recruited in Ho Chi Minh City (HCMC), Vietnam, to investigateMtbdiversity, the prevalence and phylodynamics of drug resistance, andin silicoresistance prediction with sequencing data. Amongst isolates tested phenotypically against first-line drugs, we observed high rates of streptomycin [STR, 37.7% (N=573/1,520)] and isoniazid resistance [INH, 25.7% (N=459/1,786)], and lower rates of resistance to rifampicin [RIF, 4.9% (N=87/1,786)] and ethambutol [EMB, 4.2% (N=75/1,785)]. Resistance to STR and INH was predicted moderately well when applying the TB-Profiler algorithm to WGS data (sensitivities of 0.81 and 0.87 respectively), while resistance to RIF and EMB was predicted relatively poorly (sensitivities of 0.70 and 0.44 respectively). Rates of multidrug-resistance [(MDR, 3.9% (N=69/1,786)], and resistance to a number of second-line drugs [Para-aminosalicylic acid (29.6% N=79/267), Amikacin (15.4% N=41/267) and Moxifloxacin (21.3%), N=57/267], were found to be high within a global context. Comparing rates of drug resistance among lineages, and exploring the dynamics of resistance acquisition through time, suggest the Beijing lineage (lineage 2.2) acquiresde novoresistance mutations at higher rates and suffers no apparent fitness cost acting to impede the transmission of resistance. We infer resistance to INH and STR to have arisen earlier, on average, than resistance to RIF, and to be more widespread across the phylogeny. The high prevalence of ‘background’ INH resistance, combined with high rates of RIF mono-resistance (20.7%, N=18/87) suggests that rapid assays for INH resistance will be valuable in this setting. These tests will allow the detection of INH mono-resistance, and will allow MDR isolates to be distinguished from isolates with RIF mono-resistance.
Real-world effectiveness of nirmatrelvir/ritonavir use for COVID-19: A population-based cohort study in Ontario, Canada
Authors: Schwartz KL , Wang J , Tadrous M , Langford BJ , Daneman N , Leung V , Gomes T , Friedman L , Daley P , Brown KA 
Published: November 2022

AbstractBackgroundOur objective was to evaluate the real world effectiveness of nirmatrelvir/ritonavir to prevent severe COVID-19 while Omicron and its subvariants predominate.MethodsWe conducted a population based cohort study in Ontario, Canada including all residents >17 years of age who tested positive for SARS-CoV-2 by PCR between 4 April and 31 August 2022. We compared nirmatrelvir/ritonavir treated patients to unexposed patients and measured the primary outcome of hospitalization or death from COVID-19, and a secondary outcome of death 1-30 days. We used weighted logistic regression to calculate weighted odds ratios (wOR) with 95% confidence intervals (CIs) using inverse probability of treatment weighting (IPTW) to control for confounding.ResultsThe final cohort included 177,545 patients with 8,876 (5.0%) exposed and 168,669 (95.0%) unexposed individuals. The groups were well balanced with respect to demographic and clinical characteristics after applying stabilized IPTW. Hospitalization or death within 30 days was lower in the nirmatrelvir/ritonavir treated group compared to unexposed individuals (2.1% vs 3.7%, wOR 0.56; 95%CI, 0.47-0.67). In the secondary analysis, the relative odds of death was also significantly reduced (1.6% vs 3.3%, wOR 0.49; 95%CI, 0.39-0.62). The number needed to treat to prevent one case of severe COVID-19 was 62 (95%CI 43 to 80). Findings were similar across strata of age, DDIs, vaccination status, and comorbidities.InterpretationNirmatrelvir/ritonavir was associated with significantly reduced risk of hospitalization and death from COVID-19 in this observational study, supporting ongoing use of this therapeutic to treat patients with mild COVID-19 at risk for severe disease.
Understanding Knowledge, Attitudes and Practices on Ebola Virus Disease: A Multi-Site Mixed Methods Survey on Preparedness in Rwanda
Authors: Karuhije Janvier , Nkeshimana Menelas , Zakham Fathiah , Hewins Benjamin , Rutayisire Justin , Martinez Gustavo S. , Kelvin David , Ndishimye Pacifique 
Published: November 2022

AbstractThe overall goal of this survey was to understand the Ebola Virus Disease (EVD) - related knowledge, attitudes, and practices (KAP) at individual, inter-personal, institutional, and societal levels in Rwanda. This cross-sectional mixed-methods survey was conducted in five selected districts: Rusizi, Karongi, Rubavu, Burera and Gasabo. Quantitative data was collected from 1,010 participants using a structured questionnaire and Kobo Collect. Qualitative data was collected from 98 participants through Key Informant Interviews and Focus Group Discussions using a semi structured interview guide. Among the 1,010 surveyed respondents, 56% were male, 70.3% were married, and 50% had primary education. An important finding was the high level of Ebola awareness and knowledge in all the five districts, with 99.6% reporting having previously heard of Ebola, which indicates previous awareness-raising efforts were successful. More than 54% of respondents indicated that Ebola is caused by a virus which originates from wild animal animals (42.1%). Furthermore, fever (85%), bleeding (87.7), and vomiting (40.2%) were cited as the primary signs and symptoms for Ebola. Most of the respondents were knowledgeable regarding prevention measures for Ebola. Despite this, 80% of the survey respondents had not received formal training or health education on Ebola. The majority of respondents (78.2%) reported having a positive attitude towards EVD survivors. Many respondents (90%) believe that the country is at risk of an EVD outbreak and about 87.8% think that they are personally at risk of contracting Ebola. Most respondents reported adopting habits that included avoiding physical contact with the patients and reducing unnecessary movements/travel throughout the Ebola-affected regions. At the community level, participants state that they participate in the sharing of Ebola-related information and reporting suspected cases to relevant authorities. Additionally, many participants know the necessary emergency contact number (114) for assistance and reporting of EVD-related information. Most respondents (97.2%) believed that it is important to be vaccinated to prevent Ebola, and around 93.3% are ready/willing to be vaccinated once the EVD vaccine is available. While the radio is the preferred source for Ebola-related information, the most trusted sources are the ministry of health and governmental institutions, such as the Rwanda Biomedical Centre. Our results show that there was high EVD-related knowledge and awareness among the general population in Rwanda. However, for strong public health awareness, preparedness, and protection, there is a need to implement public sensitization programmes that address EVD-related misconceptions and discriminatory attitudes toward EVD patients.
WITHDRAWN: Application of diagnostic network optimization in Kenya and Nepal to design integrated, sustainable and efficient bacteriology and antimicrobial resistance surveillance networks
Authors: Brunetti Marie , Singh Amit , Chebore Sheilla , Gyenwali Deepak , Malou Nada , Ferreyra Cecilia , Gompo Tulsi Ram , Acharya Jyoti , Rijal Nisha , Githii Susan , Wesangula Evelyn , Albert Heidi 
Published: November 2022

Withdrawal StatementThe authors have withdrawn this manuscript as it contains data that did not have the proper permissions to be publicly distributed. Therefore, the authors do not wish this work to be cited as a reference for the project. Please refer to the published version under DOI: 10.1371/journal.pgph.0002247. If you have any questions, please contact the corresponding author.
Conversational AI facilitates mental health assessments and is associated with improved recovery rates
Authors: Rollwage Max , Juchems Keno , Habicht Johanna , Carrington Ben , Hauser Tobias , Harper Ross 
Published: November 2022

AbstractMental health services across the globe are overburdened due to increased patient need for psychological therapies and a shortage of qualified mental health practitioners. This is unlikely to change in the short- to-medium term. Digital support is urgently needed to facilitate access to mental healthcare whilst creating efficiencies in service delivery. In this paper, we evaluate the use of a conversational artificial intelligence (AI) solution (Limbic Access) to assist both patients and mental health practitioners around referral, triage, and clinical assessment of mild-to-moderate adult mental illness. Assessing this solution in the context of England’s NHS Improving Access to Psychological Therapies (IAPT) services, we demonstrate that deploying such an AI solution is associated with improved recovery rates. We find that those IAPT services that introduced the conversational AI solution improved their recovery rates, while comparable IAPT services across the country reported deteriorating recovery rates during the same time period. Further, we provide an economic analysis indicating that the usage of this AI tool can be highly cost-effective relative to other methods of improving recovery rates. Together, these results highlight the potential of AI solutions to support mental health services in the delivery of quality care in the context of worsening workforce supply and system overburdening.Author summaryIn this paper, we evaluate the use of a conversational artificial intelligence solution (Limbic Access) to assist both patients and mental health practitioners around referral, triage, and clinical assessment of mild-to-moderate adult mental illness. Assessing this solution in the context of England’s NHS mental health services, we demonstrate that deploying such an AI solution is associated with improved recovery rates. We find that those services that introduced the conversational AI solution improved their recovery rates, while comparable mental health services across the country reported declining recovery rates during the same time period. Further, we provide an economic analysis indicating that the usage of this AI tool can be highly cost-effective relative to other methods of improving recovery rates. Together, these results highlight the potential of AI solutions to support mental health services in the delivery of quality care in the context of reduced workforce supply and an overburdened system.