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Nevin Manimala Statistics

Relationship between COVID-19 cases and vaccination rates in New York State counties

Ann Fam Med. 2022 Apr 1;(20 Suppl 1). doi: 10.1370/afm.20.s1.3134.

ABSTRACT

Context: The presence of new viral variants, in combination with the relaxation of social distancing and other preventative measures, has led to a spike in COVID-19 cases in the United States. The development of COVID-19 vaccinations may reduce the impact of these viral variants on case rates in the population. Objective: To determine the impact of COVID-19 vaccination rates on cases/100k population in each New York State (NYS) county. Study Design: Cross-sectional analysis of COVID-19 cases/100k population per NYS county, frozen at a single snapshot in time. Descriptive statistics and bivariate correlations were conducted to determine vaccination rates across 62 NYS counties, and linear regression was used to examine the effect of vaccination rates on cases/100k, controlling for size of county population. Dataset & Setting: Vaccination rates per county shared by the NYS Department of Health using data reported to the NYS Immunization Information System and the New York City Citywide Immunization Registry. COVID-19 case rates per county available through the John Hopkins University website. Population: NYS residents across 62 counties on March 31st, 2021. Outcome Measures: COVID-19 vaccination rates across counties at a single point in time were compared with cases/100k population. Results: Percentages with 1 dose and with 2 doses are highly correlated (r=.935, p<.001) with one another, and county population size was strongly correlated with cases per 100k (r=.715, p<.001). Both the 1 dose and 2 dose rates were negatively correlated with cases per 100k population, although not significantly. However, the two-dose vaccination rate was a significant negative predictor of cases per 100k population in NYS Counties (β= -.866, p=.031), with each percentage point of completed vaccination nearly equating to one case less in the daily count, when controlling for county population size (β =2.732, p<.001). Conclusion: While COVID-19 variants may impact vaccine effectiveness, current vaccination efforts are helping forestall some cases in NYS. Widespread vaccination is still an important goal. Primary care providers, public officials, and public health scientists should continue to urgently promote and support vaccination efforts.

PMID:36706247 | DOI:10.1370/afm.20.s1.3134

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Nevin Manimala Statistics

Recommendations for virtual care in primary care practices: a survey of patients across Ontario, Canada

Ann Fam Med. 2022 Apr 1;(20 Suppl 1). doi: 10.1370/afm.20.s1.2947.

ABSTRACT

Context: The onset of COVID-19 has required the rapid adoption of virtual services in primary care (PC) practices, and virtual care delivery is likely to continue to some extent post-pandemic. Objective: To understand patient experience with synchronous virtual (telephone (Tel)/Video) appointments and elicit recommendations for its future use. Design: Mixed method, including patient survey co-developed with stakeholders and implemented online Feb-Mar 2021 with large promotional efforts through social media, patient and caregiver organizations, and other networks. We report on the survey results. Eligibility: 1+ virtual encounter in PC. Outcome measures: A) Patient experience scale (12/17 questions for Tel/Video) covering 4 sub-dimensions; B) Access related questions. Questions had 5-point Likert scale items (strongly disagree (-2) to strongly agree (+2)) and were converted into percentage (potential range -100%, +100%) Setting : Ontario, Canada which offers universal coverage for PC visits with no co-payment. Results: 534 eligible respondents (402/18/114 had Tel/Video/both): Females (78%), < 55 years (61%), white (75%), employed (61%), bachelor’s degree (74%), family income > 100k (52%). Encounters evaluated were with family physicians (vs other health professionals) for 75%/46% of Tel/Video encounters. A) Patient Experience (Tel/Video) overall score: 75%/78%; Sub-dimensions: technology: 92%/84%, patient-provider relationship: 83%/86%, quality of care: 66%/66%, whole-person care: 43%/53%. Factors associated with a statistically significant(*) > 10% higher overall score in tel and/or video were: non-females: (8%*/14%*), French speaking (13%*/16%*), patient-provider relationship >1 year (16%*/7%), provider age < 50 (5%/15%*), having the choice of appointment time (15%*/21%*). Wanting to show problem to the provider was associated with a lower scores (-23%*/NA). B) Access Respondents overwhelmingly reported that Tel/Video visits reduced time (97%/97%), costs (81%/85%), and was more convenient (91%/91%). The majority wanted Tel (69%) and Video (71%) visits at least as often as in person visits post-covid. Only 5% did not want any future virtual care. Conclusions: Patient experience was largely positive and is influenced by patient/provider factors. Patients and providers may benefit from support/training to optimize care experience. We are now evaluating whether the reasons for visits influences care experience.

PMID:36706237 | DOI:10.1370/afm.20.s1.2947

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Nevin Manimala Statistics

Time series transcriptome analysis implicates the circadian clock in the Drosophila melanogaster female’s response to sex peptide

Proc Natl Acad Sci U S A. 2023 Jan 31;120(5):e2214883120. doi: 10.1073/pnas.2214883120. Epub 2023 Jan 27.

ABSTRACT

Sex peptide (SP), a seminal fluid protein of Drosophila melanogaster males, has been described as driving a virgin-to-mated switch in females, through eliciting an array of responses including increased egg laying, activity, and food intake and a decreased remating rate. While it is known that SP achieves this, at least in part, by altering neuronal signaling in females, the genetic architecture and temporal dynamics of the female’s response to SP remain elusive. We used a high-resolution time series RNA-sequencing dataset of female heads at 10 time points within the first 24 h after mating to learn about the genetic architecture, at the gene and exon levels, of the female’s response to SP. We find that SP is not essential to trigger early aspects of a virgin-to-mated transcriptional switch, which includes changes in a metabolic gene regulatory network. However, SP is needed to maintain and diversify metabolic changes and to trigger changes in a neuronal gene regulatory network. We further find that SP alters rhythmic gene expression in females and suggests that SP’s disruption of the female’s circadian rhythm might be key to its widespread effects.

PMID:36706221 | DOI:10.1073/pnas.2214883120

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Nevin Manimala Statistics

Utilization of Transport Data to Decrease Unnecessarily Repeated Laboratory Tests

Pediatr Emerg Care. 2023 Jan 24. doi: 10.1097/PEC.0000000000002730. Online ahead of print.

ABSTRACT

OBJECTIVES: In pediatric patients being transported for management of diabetic ketoacidosis, laboratory tests will frequently be trended throughout transportation and subsequently immediately repeated upon arrival to a particular institution. These laboratory tests may not add value to a patient’s care trajectory and therefore may be unnecessary. This study examines differences between pH, sodium, potassium, chloride, bicarbonate, and glucose levels drawn during transportation and those drawn at our home institution immediately upon arrival to determine if repeating those laboratory tests upon arrival to the emergency department serves any purpose in adding to patient care.

METHODS: This study compares pH, sodium, potassium, chloride, bicarbonate, and glucose levels drawn during transport and at our home institution. Box and whisker plots between transport and institution laboratory values were constructed. A Wilcoxon signed rank test was performed to determine differences between pH, sodium, potassium, bicarbonate, and glucose levels, as these value sets were not normally distributed. A paired t test was performed to determine differences between transport and institution chloride values given that these value sets were normally distributed. Savings were then calculated based on charges to the patient to determine overall cost savings by not immediately repeating these laboratory tests upon presentation.

RESULTS: Box and whisker plots showed marked similarity between laboratory tests drawn in transport and those immediately upon arrival to our ED. Paired t test did not demonstrate a statistical difference between transport and ED chloride levels (P = 0.5699); therefore, we failed to reject the null hypothesis. Wilcoxon signed rank test did not demonstrate a statistical difference between transport and ED pH (P = 0.1294) and potassium (P = 0.4523) values; therefore, we failed to reject the null hypothesis. However, Wilcoxon signed rank test did demonstrate a statistically significant difference between uncorrected sodium (P = 0.0006), corrected sodium (P = 0.0075), bicarbonate (P = <0.0001), and glucose levels (P = 0.0086).

CONCLUSIONS: Although there were some statistically significant differences between the laboratory value sets, it is arguable whether there are any clinically significant differences between them.Based on our failure to show a clinically significant difference between laboratory values drawn during transportation and those drawn immediately upon presentation to the institution, repeating laboratory draws after transportation do not add value to a patient’s care trajectory. We should therefore rely on the laboratory values that were drawn from our transportation teams as part of the continuum of patient care.

PMID:36706218 | DOI:10.1097/PEC.0000000000002730

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Nevin Manimala Statistics

Self-perception of physical appearance of adolescents and associated factors in Addis Ababa, Ethiopia

PLoS One. 2023 Jan 27;18(1):e0281202. doi: 10.1371/journal.pone.0281202. eCollection 2023.

ABSTRACT

INTRODUCTION: Establishing a positive body image is a critical factor for adolescents’ physical and mental health, as it determines self-confidence, and sustainable individual growth and development throughout their lives. This reality needs to be supported by evidences generated locally. However, there is a lack of information in this regard in the study setting. Thus, the aim of this study was to assess the self-perception of one’s physical appearance and its associated factors among adolescents in Addis Ababa, Ethiopia.

METHODS AND MATERIALS: A community-based, cross-sectional study design was used to conduct the study. At the end of the multistage sampling procedure, a systematic random sampling technique was employed to select 308 study participants from selected districts. The questionnaire was adapted from previous studies as it was appropriate for local context. The data collectors were trained before the data collection and supervised during the data collection period, and the questionnaire was pretested. Bivariate logistic regression was used to identify candidate variables, and then variables with p<0.2 were taken to multiple logistic regressions to identify independent associated factors. Statistical significance was considered at P <0.05 with adjusted odds ratios calculated at 95% CIs.

RESULT: A total of 283 adolescents were participated in the study, with a response rate of 91.9%. The overall good self-perception of one’s physical appearance was 48.4% [95% CI = 43.8, 54.1]. Having a BMI between 18.5 kg/m2-24.9 kg/m2 (AOR = 2.56; 95% CI: 1.45, 4.54), presence of enough sport fields in the school (AOR = 1.89; 95% CI: 1.09, 3.29), having daily access to internet services (AOR = 1.69; 95% CI: 1.07, 2.94), following Ethiopian movies/cinemas (AOR = 2.46; 95% CI: 1.46, 4.15), and regularly following western movies/cinemas (AOR = 2.0; 95% CI: 1.11, 3.59) were significantly associated with a good self-perception of one’s physical appearance.

CONCLUSION: According to this study, only 48.4% of respondents reported a good self-perception of their physical appearance. Adolescents and their family need to work to bring normal body mass index, which in turn will increase good self-perceptions of their physical appearance. Schools and the local administrations need to increase availability and access to enough sport fields for students to strengthen their physical fitness, which increases their good self-perception of their physical appearance.

PMID:36706128 | DOI:10.1371/journal.pone.0281202

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Nevin Manimala Statistics

Does hand proximity enhance letter identification?

PLoS One. 2023 Jan 27;18(1):e0280991. doi: 10.1371/journal.pone.0280991. eCollection 2023.

ABSTRACT

Adam et al. (2012) found that letters were identified more accurately when presented near, compared to away from, the hands. Participants performed the task in two conditions: with their hands held stationary and with their hands moving towards and away from the target letters. The near-hands effect included the contribution of both static and dynamic trials. Further studies showed that accuracy in letter discrimination was higher when hands were away from a target (a far-hands effect) and moving toward it, suggesting an interaction between hand position and movement direction. The present study aimed to test whether hand proximity affects letter identification when the hands are stationary, as it remains unclear if this effect can be reliably observed. Participants viewed strings of three consonants, briefly presented and masked, and had to verbally report their identity. Stimuli were presented under two different hand conditions: proximal and distal. The predicted effects of letter position and stimulus duration were all statistically significant and robust; however, we did not observe a hand proximity effect.

PMID:36706115 | DOI:10.1371/journal.pone.0280991

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Nevin Manimala Statistics

When months matter; modelling the impact of the COVID-19 pandemic on the diagnostic pathway of Motor Neurone Disease (MND)

PLoS One. 2023 Jan 27;18(1):e0259487. doi: 10.1371/journal.pone.0259487. eCollection 2023.

ABSTRACT

BACKGROUND: A diagnosis of MND takes an average 10-16 months from symptom onset. Early diagnosis is important to access supportive measures to maximise quality of life. The COVID-19 pandemic has caused significant delays in NHS pathways; the majority of GP appointments now occur online with subsequent delays in secondary care assessment. Given the rapid progression of MND, patients may be disproportionately affected resulting in late stage new presentations. We used Monte Carlo simulation to model the pre-COVID-19 diagnostic pathway and then introduced plausible COVID-19 delays.

METHODS: The diagnostic pathway was modelled using gamma distributions of time taken: 1) from symptom onset to GP presentation, 2) for specialist referral, and 3) for diagnosis reached after neurology appointment. We incorporated branches to simulate delays: when patients did not attend their GP and when the GP consultation did not result in referral. An emergency presentation was triggered when diagnostic pathway time was within 30 days of projected median survival. Total time-to-diagnosis was calculated over 100,000 iterations. The pre-COVID-19 model was estimated using published data and the Improving MND Care Survey 2019. We estimated COVID-19 delays using published statistics.

RESULTS: The pre-COVID model reproduced known features of the MND diagnostic pathway, with a median time to diagnosis of 399 days and predicting 5.2% of MND patients present as undiagnosed emergencies. COVID-19 resulted in diagnostic delays from 558 days when only primary care was 25% delayed, to 915 days when both primary and secondary care were 75%. The model predicted an increase in emergency presentations ranging from 15.4%-44.5%.

INTERPRETATIONS: The model suggests the COVID-19 pandemic will result in later-stage diagnoses and more emergency presentations of undiagnosed MND. Late-stage presentations may require rapid escalation to multidisciplinary care. Proactive recognition of acute and late-stage disease with altered service provision will optimise care for people with MND.

PMID:36706102 | DOI:10.1371/journal.pone.0259487

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Nevin Manimala Statistics

What percentage of patients with cancer develop hiccups with oxaliplatin- or cisplatin-based chemotherapy? a compilation of patient-reported outcomes

PLoS One. 2023 Jan 27;18(1):e0280947. doi: 10.1371/journal.pone.0280947. eCollection 2023.

ABSTRACT

BACKGROUND: Chemotherapy-induced hiccups are understudied but can cause sleep deprivation, fatigue, pain in the chest and abdomen, poor oral intake, aspiration, and even death. As a critical next step toward investigating better palliative methods, this study reported patient-reported incidence of hiccups after oxaliplatin- or cisplatin-based chemotherapy.

METHODS: The current study relied on 2 previous studies that sought to acquire consecutive direct patient report of hiccups among patients who had recently received chemotherapy with cisplatin or oxaliplatin. These patient-reported data in conjunction with information from the medical record are the focus of this report.

RESULTS: Of 541 patients, 337 were successful contacted by phone; and 95 (28%; 95% CI: 23%, 33%) of these contacted patients reported hiccups. In univariable analyses, male gender (odds ratio (OR): 2.17 (95% confidence ratio (95% CI): 1.30, 3.62); p = 0.002), increased height (OR: 1.03 (95% CI: 1.00, 1.06); p = 0.02), and concomitant aprepitant/fosaprepitant (OR: 2.23 (95% CI: 1.31, 3.78); p = 0.002) were associated with hiccups. In multivariable analyses, these statistically significant associations persisted except for height.

CONCLUSIONS: These patient-reported data demonstrate that oxaliplatin- or cisplatin-induced hiccups occur in a notable proportion of patients with cancer. Male gender and concomitant aprepitant/fosaprepitant appear to increase risk.

PMID:36706101 | DOI:10.1371/journal.pone.0280947

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Nevin Manimala Statistics

Proteomic Predictors of Incident Diabetes: Results From the Atherosclerosis Risk in Communities (ARIC) Study

Diabetes Care. 2023 Jan 27:dc221830. doi: 10.2337/dc22-1830. Online ahead of print.

ABSTRACT

OBJECTIVE: The plasma proteome preceding diabetes can improve our understanding of diabetes pathogenesis.

RESEARCH DESIGN AND METHODS: In 8,923 Atherosclerosis Risk in Communities (ARIC) Study participants (aged 47-70 years, 57% women, 19% Black), we conducted discovery and internal validation for associations of 4,955 plasma proteins with incident diabetes. We externally validated results in the Singapore Multi-Ethnic Cohort (MEC) nested case-control (624 case subjects, 1,214 control subjects). We used Cox regression to discover and validate protein associations and risk-prediction models (elastic net regression with cardiometabolic risk factors and proteins) for incident diabetes. We conducted a pathway analysis and examined causality using genetic instruments.

RESULTS: There were 2,147 new diabetes cases over a median of 19 years. In the discovery sample (n = 6,010), 140 proteins were associated with incident diabetes after adjustment for 11 risk factors (P < 10-5). Internal validation (n = 2,913) showed 64 of the 140 proteins remained significant (P < 0.05/140). Of the 63 available proteins, 47 (75%) were validated in MEC. Novel associations with diabetes were found for 22 the 47 proteins. Prediction models (27 proteins selected by elastic net) developed in discovery had a C statistic of 0.731 in internal validation, with ΔC statistic of 0.011 (P = 0.04) beyond 13 risk factors, including fasting glucose and HbA1c. Inflammation and lipid metabolism pathways were overrepresented among the diabetes-associated proteins. Genetic instrument analyses suggested plasma SHBG, ATP1B2, and GSTA1 play causal roles in diabetes risk.

CONCLUSIONS: We identified 47 plasma proteins predictive of incident diabetes, established causal effects for 3 proteins, and identified diabetes-associated inflammation and lipid pathways with potential implications for diagnosis and therapy.

PMID:36706097 | DOI:10.2337/dc22-1830

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A Mobile Health App (ChillTime) Promoting Emotion Regulation in Dual Disorders: Acceptability and Feasibility Pilot Study

JMIR Form Res. 2023 Jan 27;7:e37293. doi: 10.2196/37293.

ABSTRACT

BACKGROUND: A growing number of studies highlight the importance of emotion regulation in the treatment and recovery of individuals with psychosis and concomitant disorders such as substance use disorder (SUD), for whom access to integrated dual-disorder treatments is particularly difficult. In this context, dedicated smartphone apps may be useful tools to provide immediate support to individuals in need. However, few studies to date have focused on the development and assessment of apps aimed at promoting emotional regulation for people with psychosis.

OBJECTIVE: The aim of this study was to evaluate the feasibility, acceptability, and potential clinical impact of a dedicated app (ChillTime) for individuals with psychotic disorders and concurrent SUD. The app design process followed recommendations for reducing cognitive effort on a mobile app. A total of 20 coping strategies regrouped in four categories (behavioral, emotional, cognitive, spiritual) were included in the app.

METHODS: This open pilot study followed a pre-post design. After the initial assessment, researchers asked participants to use the app as part of their treatment over a 30-day period. Feasibility was determined by the frequency of use of the app and measured using the number of completed strategies. Acceptability was determined by measuring ease of use, ease of learning, satisfaction, and perceived utility at the end of the 30-day study period based on responses to satisfaction questionnaires. Clinical scales measuring emotion regulation, substance use (ie, type of substance, amount taken, and frequency of use), and various psychiatric symptoms were administered at the beginning and end of the 30-day period.

RESULTS: A total of 13 participants were recruited from two first-episode psychosis clinics in Montreal, Quebec, Canada. All participants were symptomatically stable, were between 18 and 35 years of age (mostly men; 70% of the sample), and had a schizophrenia spectrum disorder with a comorbid substance use diagnosis. A total of 11 participants completed the study (attrition<20%). Approximately half of the participants used the tool at least 33% of the days (11-21 days). Cognitive and emotion-focused techniques were rated the highest in terms of usefulness and were the most frequently used. The majority of participants gave positive answers about the ease of use and the ease of learning the tool. A nonsignificant association of ChillTime use with negative symptoms and drug use was observed. No other statistically significant changes were observed.

CONCLUSIONS: The ChillTime app showed good feasibility (approximately half of the participants used the tool at least 33% of the days) and acceptability among people with schizophrenia spectrum disorder and SUD. Trends suggesting a potential impact on certain clinical outcomes will need to be replicated in larger-sample studies before any conclusion can be drawn.

PMID:36705963 | DOI:10.2196/37293