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1.
Contemp Clin Trials ; 143: 107609, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38878996

ABSTRACT

BACKGROUND: Burnout in primary care undermines worker well-being and patient care. Many factors contribute to burnout, including high workloads, emotional stress, and unsupportive supervisors. Formative evidence suggests that burnout might be reduced if clinic leaders hold quarterly and brief (∼30 min) one-on-one check-ins with team members to acknowledge and address work-life stressors (e.g., schedules, workflow breakdowns, time off requests). This paper describes the intervention protocol for a randomized controlled trial (RCT) designed to evaluate the effectiveness and process of the check-ins in reducing burnout among primary care professionals. METHODS: Two-arm RCT conducted at 12 primary care clinics of a healthcare system in the Pacific Northwest. Six clinics received an adaptive design, semi-structured intervention, including predefined training modules with evidence-based tactics to reduce burnout through the check-ins, followed by clinic-specific feedback sessions prior to offering and conducting quarterly leader-employee check-ins. Six clinics were randomized as waitlist controls. Burnout was measured using the Maslach Burnout Inventory (MBI) at baseline and at the 12-month follow-up. Secondary outcomes include organizational constraints, psychological safety, and supervisor support. Multilevel modeling and qualitative methods were applied to evaluate the effects and process of the intervention. CONCLUSION: By focusing on modifiable work-life factors such as stressors and supervisor support, the check-ins intervention aims to reduce burnout rates among primary care professionals. Findings from this trial will shed light on the conditions upon which check-ins might reduce burnout. Results will also inform policies and interventions aimed at improving mental health and well-being in primary care settings. CLINICALTRIALS: gov: ID NCT05436548.


Subject(s)
Burnout, Professional , Leadership , Primary Health Care , Adult , Female , Humans , Male , Burnout, Professional/prevention & control , Primary Health Care/organization & administration , Workload/psychology , Randomized Controlled Trials as Topic
2.
Enferm Clin (Engl Ed) ; 34(4): 250-258, 2024.
Article in English | MEDLINE | ID: mdl-38642837

ABSTRACT

OBJECTIVE: To assess the effectiveness and safety of a topical silicone gel (BE + Gel reductor y reparador de cicatrices) and a polyurethane dressing (BE + Apósito reductor y reparador de cicatrices) on the evolution of scars of patients who were previously recruited in the emergency care unit while seeking wound care. METHOD: A single center, stratified observational, open label study was performed in the emergency care unit of Donostia Universitary Hospital (recruitment) and in the Biodonostia Health Research Institute (intervention). Scars located in unexposed body areas with the dressing, and scars located in exposed areas with either the gel or the dressing. Investigators assessed interventions at day 1 and on weeks 4, 8 and 12. Vancouver Scar Scale (VSS) and a photographical assessment were used to determine the scars evolution, and the subjective perception of the scar was evaluated by means of a questionnaire administered to the patients. RESULTS: Patients whose scars were treated with the silicone gel had an average initial VSS score of 5.4 ± 2.08. This value was reduced to 0.86 ± 1.17 after 90 days of treatment. Patients treated with the polyurethane dressing had an average initial VSS score of 5.8 ± 2.29. After 90 days of treatment, this average score was reduced to 0.33 ± 0.66. Positive evolution of scars was also supported by photographs and by a patient questionnaire. CONCLUSIONS: Both treatments appear to be safe and effective, objectively, and subjectively, in the context of scar evolution.


Subject(s)
Bandages , Cicatrix , Polyurethanes , Silicone Gels , Humans , Polyurethanes/administration & dosage , Female , Silicone Gels/administration & dosage , Silicone Gels/therapeutic use , Male , Middle Aged , Adult , Aged , Administration, Topical , Treatment Outcome , Young Adult
3.
Lancet Reg Health Am ; 31: 100705, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38445021

ABSTRACT

Background: Reducing maternal mortality ratio (MMR) remains a paramount goal for low- and middle-income countries (LMICs), especially after COVID-19's devastating impact on maternal health indicators. We describe our experience implementing the Hospital Padrino Strategy (HPS), a collaborative model between a high-complexity hospital (Fundación Valle del Lili) and 43 medium- and low-complexity hospitals in one Colombian department (an administrative and territorial division) from 2021 to 2022, to sustain the trend towards reducing MMR. The study aimed to assess the effects of implementing HPS on both hospital performance and maternal health indicators in Valle del Cauca department (VCD). Methods: A mixed-methods study was conducted, comprising two phases. In the first phase, we investigated a cohort of hospitals through prospective follow-up to assess the outcomes of HPS implementation on hospital performance and maternal health indicators in VCD. In the second phase, qualitative data were collected through focus groups with 131 health workers from 33 hospitals to explore the implications of the HPS implementation on healthcare personnel. All data were obtained from records within the HPS implementation and from the Health Secretary of VCD. Findings: Evidence shows that in the context of HPS, 51 workshops involved 980 healthcare workers, covering the entire territory. Substantial improvements were observed in hospital conditions and healthcare personnel's technical competencies when providing obstetric care. Seven hundred eighty-five pregnant women with obstetric or perinatal emergencies received care through telehealth systems, with a progressive increase in technology adoption. Nine percent required Intensive Care Unit (ICU) admission, and none died. The MMR decreased from 78.8 in 2021 to 12.0 cases per 100,000 live births by 2022. Improvements in indicators and conducted training sessions instilled confidence and empowerment among the healthcare teams in the sponsored hospitals, as evidenced in focus groups derived from a sample of 131 healthcare workers from 33 hospitals. Interpretation: Implementing the Hospital Padrino Strategy led to a significant MMR reduction, and consolidated a model of social healthcare innovation replicable in LMICs. Funding: The Hospital Padrino Strategy was funded by the Fundación Valle del Lili and the Health Secretary of Valle del Cauca. Furthermore, this study received funding from a general grant for research from Tecnoquimicas S.A.

4.
Sci Rep ; 14(1): 3544, 2024 02 12.
Article in English | MEDLINE | ID: mdl-38347059

ABSTRACT

Acute poisonings are a global public health problem, which implies costs and disease burden for society. In Colombia, there is a significant underreporting of data on acute poisoning and data gaps on the toxicological profile of the population. This study aims to identify the epidemiology of acute poisoning in a high-complexity hospital in southwestern Colombia. A descriptive study with retrospective data collection was performed. The variables were expressed through the measure of central tendency and dispersion. Categorical variables were described in proportions. A total of 406 patients were included. The median age was 31 years (IQR 23-48), 56.2% were male, and only 19.2% had a history of mental illness. Suicidal intent represented 58.8% of the cases, and the most frequent route of exposure was the oral route (81.6%). The most prevalent groups of substances were pesticides (34.2%) and medicines (32%). The most common etiological agent was organophosphates (16.5%). Cholinergic toxidrome was the most common. The average stay in the ICU was 4.5 days (± 4.8), and the mortality was 4.2%. The principal causes of acute poisoning were drugs and pesticides, with a predominant etiology of organophosphates and depressants of the central nervous system. There was a significant predominance of young male patients with suicidal intent, low mental disorders, elevated unemployment rate, and similar mortality reported in other studies. This study improves the knowledge about acute poisoning in southwestern Colombian to carry out multicenter analytic studies.


Subject(s)
Pesticides , Poisoning , Adult , Female , Humans , Male , Colombia/epidemiology , Emergency Service, Hospital , Hospitals, University , Organophosphates , Retrospective Studies
5.
Am J Public Health ; 114(S2): 204-212, 2024 02.
Article in English | MEDLINE | ID: mdl-38354349

ABSTRACT

Objectives. The COVID-19 pandemic imposed unprecedented safety challenges on health care facilities. This study examined whether health care workers who deemed a better safety response to the pandemic by their units or employers experienced lower psychological distress. Methods. Patient care workers at a health care system in the Pacific Northwest were surveyed every 6 to 8 months from May 2020 to May 2022 (n = 3468). Psychological distress was measured with the Well-being Index (range: -2 to 7 points). Safety response was scored on the basis of participants' ratings (on a 1-5 scale) of equipment sufficiency and responsiveness to safety concerns by their health care system and unit. Results. Adjusted multilevel regressions showed an inverse association between safety responsiveness and psychological distress at the individual level (b = -0.54; 95% confidence interval [CI] = -0.67, -0.41) and the unit level (b = -0.73; 95% CI = -1.46, -0.01). The cross-level interaction was also statistically significant (b = -0.46; 95% CI = -0.87, -0.05). Conclusions. Health care workers who deemed a better response to safety challenges reported lower psychological distress. This study highlights the need for continued efforts to ensure adequate safety resources. (Am J Public Health. 2024;114(S2):S204-S212. https://doi.org/10.2105/AJPH.2024.307582).


Subject(s)
COVID-19 , Psychological Distress , Humans , COVID-19/epidemiology , Pandemics , Health Personnel/psychology , Delivery of Health Care
6.
Mayo Clin Proc ; 98(6): 856-867, 2023 06.
Article in English | MEDLINE | ID: mdl-37024355

ABSTRACT

OBJECTIVE: To analyze the role of short (<30 minutes) and frequent (quarterly) check-ins between clinic leaders and employees in reducing emotional exhaustion. METHODS: Three interrelated studies were conducted: a 3-year repeated cross-sectional survey at 10 primary care clinics (n=505; we compared emotional exhaustion, perceived stress, and values alignment among employees of a clinic where check-ins were conducted vs 9 control clinics); interviews with leaders and employees (n=10) regarding the check-ins process and experiences; and interviews with leaders and employees (n=10) after replicating the check-ins at a new clinic. RESULTS: Outcomes were similar at baseline. After a year, emotional exhaustion was lower at the check-ins compared with control clinics (standardized mean difference, d, -0.71 [P<.05]). After 2 years, emotional exhaustion remained lower at the check-ins clinic, but this difference was not significant. The check-ins were associated with an increment in values alignment (2018 vs 2017, d=0.59 [P<.05]; 2019 vs 2017, d=0.76 [P<.05]). There were no differences for perceived job stress. Interviews indicated that work-life challenges were discussed in the check-ins. However, employees need confidentiality and to feel safe to do so. The replication suggested that the check-ins are feasible to implement even amid turbulent times. CONCLUSION: Periodic check-ins wherein leaders acknowledge and address work-life stressors might be a practical tactic to reduce emotional exhaustion in primary care clinics.


Subject(s)
Emotions , Occupational Stress , Humans , Cross-Sectional Studies , Occupational Stress/prevention & control , Primary Health Care
7.
Cureus ; 15(1): e34172, 2023 Jan.
Article in English | MEDLINE | ID: mdl-36843782

ABSTRACT

Multiple myeloma (MM) is a common hematologic malignancy. Multi-agent chemotherapy and anti-myeloma immunomodulatory drugs increase the incidence of arterial and venous thrombosis. We present a moyamoya patient with MM who had a stroke shortly after induction chemotherapy. We present the case of an adult female patient who arrived at the ER due to automatism seizures, dysarthria, and left hemiparesis. The patient had a medical history of MM and underwent six cycles of induction chemotherapy (cyclophosphamide, dexamethasone, thalidomide, and bortezomib). MRI of the brain showed bilateral watershed ischemic strokes. Angiogram showed occlusion at the supraclinoid segment of both internal carotid arteries consistent with moyamoya. The patient was discharged with full-dose anticoagulation, levetiracetam, and physical therapy. At three years of follow-up, the patient has no recurrent cerebrovascular disease. MM patients treated with thalidomide/lenalidomide in combination with high-dose dexamethasone, doxorubicin, or multiagent chemotherapy should be on anticoagulation for venous thromboembolism (VTE) prophylaxis. There are no clear recommendations for arterial thrombosis prevention. Moyamoya is a vasculopathy characterized by progressive intracranial artery stenosis with a high risk of ischemic stroke, ischemia recurrence, and intracerebral hemorrhage. Despite the risk of intracerebral hemorrhage, we decided on anticoagulation due to the high risk of thrombosis due to MM, multi-agent chemotherapy, and moyamoya.

8.
Entramado ; 17(2): 292-304, jul.-dic. 2021. tab
Article in Spanish | LILACS-Express | LILACS | ID: biblio-1360429

ABSTRACT

RESUMEN Se realizó un estudio observacional de corte transversal con enfoque descriptivo con el objetivo de determinar el riesgo por exposición a agentes químicos, atmósferas peligrosas y definir recomendaciones para mejorar las condiciones de trabajo en las minas de carbón de Tópaga (Boyacá). Para recopilar la información se utilizó el cuestionario para la identificación y prevención del riesgo en espacios confinados, del Instituto Nacional de Seguridad e Higiene en el Trabajo, y se realizaron mediciones de gases en las minas. Los resultados muestran que el 25% de las minas tienen niveles de oxígeno inferiores a 19,5% y ninguna supera el límite de explosividad. El 15% supera el Valor Límite Permisible (VLP) de monóxido de carbono y el 20% supera el VLP de sulfuro de hidrógeno y dióxido de azufre. Entre las recomendaciones propuestas se encuentra favorecer la ventilación natural, aplicar ventilación forzada cuando la natural resulte insuficiente y el empleo de calzado y herramientas antichispa. Se concluye que, en general, las condiciones de trabajo en las minas son inadecuadas para la seguridad y salud de los mineros.


ABSTRACT An observational cross-sectional study with a descriptive approach was carried out with the objective of determining the risk due to exposure to chemical agents, dangerous atmospheres and defining recommendations to improve working conditions in the coal mines of Tópaga (Boyacá). During the data collection process was used the questionnaire for the identification and prevention of risk in confined spaces, of the National Institute of Safety and Hygiene at Work. Moreover gas measurements were made in the mines. The results show that 25% of the mines have oxygen levels below 19.5% and none exceed the explosive limit. 15% exceed the Permissible Limit Value (VLP) for carbon monoxide and 20% exceed the VLP for hydrogen sulfide and sulfur dioxide. The proposed recommendations include favoring natural ventilation, applying forced ventilation when the natural one is insufficient and the use of non-sparking shoes and tools. It is concluded that, in general, the working conditions in the mines are inadequate for the safety and health of the miners.


RESUMO Foi realizado um estudo observacional transversal com abordagem descritiva com o objetivo de determinar o risco devido à exposição a agentes químicos, atmosferas perigosas e definir recomendações para melhorar as condições de trabalho nas minas de carvão de Tópaga em Boyacá. Para colher as informações, foi utilizado o questionário de identificação e prevenção de riscos em espaços confinados, do Instituto Nacional de Segurança e Higiene no Trabalho, e realizaram medidas do nível dos gases nas minas visitadas. Os resultados mostram que 25% das minas apresentam níveis de oxigênio abaixo de 19,5% e nenhuma excede o limite explosivo. 15% excedem o valor limite permitido (VLP) para o monóxido de carbono e 20% excedem o VLP para o sulfeto de hidrogênio e dióxido de enxofre. Entre as recomendações propostas estão favorecer a ventilação natural, aplicar ventilação forçada quando a ventilação natural for insuficiente e o uso de calçados e ferramentas anti-faísca. Conclui-se que, em geral, as condições de trabalho nas minas são inadequadas para a segurança e a saúde dos mineiros.

9.
Am J Ind Med ; 64(2): 137-148, 2021 02.
Article in English | MEDLINE | ID: mdl-33094485

ABSTRACT

BACKGROUND: Firefighters endure large occupational burdens and generally operate under conditions of chronic sleep deficiency and circadian disruption due to long shifts, plus interrupted sleep due to emergency calls during the night. A typical shift for firefighters is 24-h on/48-h off, and firefighters are expected to use time-off to recover from any sleep debt, while balancing social, family, and home responsibilities. This qualitative study sets out to assess family dynamics and how firefighters prioritize sleep and recovery at home based on relationship or family status, as well as a fire department's current shift schedule. METHODS: Focus groups were conducted via convenience sampling in Portland, OR, with full-time firefighters, battalion chiefs, and their spouses. Grounded theory, using NVivo 12 Plus, was used to code transcripts to reveal reoccurring concepts and themes. RESULTS: Major themes centered around the increase of nonemergent calls contributing to compassion fatigue. Spouses can help improve the sleep of firefighters by creating opportunities for recuperative sleep at home. However, spouses also conveyed underlying tones of "resentment" relating to their firefighter being unavailable for emotional and instrumental support. While married firefighters discussed choosing family and home obligations over reducing sleep debt to maintain relationships, single and divorced firefighters spoke of fewer conflicts impeding their ability to prioritize sleep at home. CONCLUSIONS: These results improve our understanding of how firefighters prioritize sleep at home based on family dynamics and can inform future decision-making for fire departments in addressing concerns related to work-family conflict, sleep loss, and compassion fatigue among their members.


Subject(s)
Compassion Fatigue/psychology , Firefighters/psychology , Occupational Diseases/psychology , Sleep Deprivation/psychology , Sleep , Adult , Female , Focus Groups , Humans , Male , Middle Aged , Oregon , Qualitative Research , Spouses/psychology , Work/psychology , Work Schedule Tolerance/psychology , Work-Life Balance
10.
Bioinformatics ; 37(3): 360-366, 2021 04 20.
Article in English | MEDLINE | ID: mdl-32780838

ABSTRACT

MOTIVATION: Proteins are ubiquitous molecules whose function in biological processes is determined by their 3D structure. Experimental identification of a protein's structure can be time-consuming, prohibitively expensive and not always possible. Alternatively, protein folding can be modeled using computational methods, which however are not guaranteed to always produce optimal results. GraphQA is a graph-based method to estimate the quality of protein models, that possesses favorable properties such as representation learning, explicit modeling of both sequential and 3D structure, geometric invariance and computational efficiency. RESULTS: GraphQA performs similarly to state-of-the-art methods despite using a relatively low number of input features. In addition, the graph network structure provides an improvement over the architecture used in ProQ4 operating on the same input features. Finally, the individual contributions of GraphQA components are carefully evaluated. AVAILABILITY AND IMPLEMENTATION: PyTorch implementation, datasets, experiments and link to an evaluation server are available through this GitHub repository: github.com/baldassarreFe/graphqa. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Subject(s)
Neural Networks, Computer , Proteins , Protein Folding
11.
Jt Comm J Qual Patient Saf ; 46(11): 608-616, 2020 11.
Article in English | MEDLINE | ID: mdl-32893178

ABSTRACT

BACKGROUND: Safe patient handling and mobility (SPHM) programs recommend having champions, but have not indicated how to identify them and have confined their role to peer-based activities, limiting their ability to influence control measures. METHODS: In a pilot program conducted at a community access hospital in Oregon, researchers applied social network analysis (SNA) of safety advice to identify champion candidates. Candidates were invited to complete mobility, communication, and quality improvement (QI) training modules to become champions. Champions' roles included peer-based instruction and participation in QI quarterly meetings with hospital leaders. The program process was evaluated through weekly e-mail check-ins and documentation of quarterly meetings. Outcomes were evaluated with a pre-post design, observing 12-month changes in self-reported leading indicators and Good Catch reports, as well as trends in patient-assist injuries (2011-2019). RESULTS: SNA identified six candidates, four of whom became champions. Champions completed 48 weekly logs. The quarterly meetings concerned unitwide SPHM training, equipment storage, and onboarding. Results showed significant improvements in equipment use, safety participation, and safety compliance, particularly among workers who would seek SPHM advice from champions or recently hired workers. Compared with the prior year, the Good Catch monthly entries increased from 11.69 to 28.81. The average annual incidence rate of patient-assist injuries dropped from 13.01 for the six years before the program to 3.7 per 100 full-time equivalents (FTE) for the two years after. CONCLUSION: A program with SNA-identified and QI-trained champions improved safety outcomes after one year. Better-designed evaluations are needed to establish the replicability and long-term impact of this program.


Subject(s)
Health Personnel , Social Network Analysis , Humans , Oregon , Peer Group , Quality Improvement
12.
Ann Work Expo Health ; 64(8): 897-902, 2020 10 08.
Article in English | MEDLINE | ID: mdl-32607532

ABSTRACT

OBJECTIVES: Workers in small and medium residential construction companies (≤50 employees) have a high risk of fall-related fatality or disability. However, little is known about effective ways to engage with this subsector for research and training. We tested whether insurance-documented fall-related claims during the past 12 months and lower familiarity with equipment motivated companies' representatives to engage with a fall protection survey. METHODS: Oregon's largest workers compensation insurer drew a random anonymous sample of small and medium residential construction that did (n = 197) and did not (n = 195) have a recent fall-related claim. Samples were stratified by size, trade, and region. Company representatives were emailed a 34-item questionnaire about equipment familiarity to enter a raffle to win fall-prevention equipment. We coded survey engagement binarily, indicating whether a participant completed at least half of the survey. Familiarity with 10 pieces of equipment was measured with a scale from 0 (never seen it) to 3 (use it frequently) points. RESULTS: The survey was initiated by 88 out of 392 representatives (22.4% response rate). Of those, 63 representatives provided the company identifier which was needed to establish claim status. Survey engagement was higher among representatives from companies with claims compared with those without (57.6 versus 42.4%, P = 0.16). Equipment familiarity was lower among company representatives with lower survey engagement (1.15 versus 1.56, P < 0.05). CONCLUSIONS: The survey had a relatively encouraging response rate for a hard-to-reach sector. The large but not statistically significant difference in survey engagement rates suggests that adverse events motivate companies to engage with fall protection research. Low equipment familiarity in the sample substantiates the need to identify effective engagement methods for fall protection practices.


Subject(s)
Accidental Falls , Accidental Falls/prevention & control , Humans , Occupational Exposure , Small Business , Surveys and Questionnaires , Workers' Compensation
13.
J Matern Fetal Neonatal Med ; 33(18): 3086-3090, 2020 Sep.
Article in English | MEDLINE | ID: mdl-30632844

ABSTRACT

Objective: The objective of this article was to compare hemodynamic and perfusion parameters as well as the clinical outcomes in critically ill patients with postpartum hemorrhage (PPH) who received treatment with a nonpneumatic antishock garment (NASG) as part of an intervention package, with a group of patients in similar conditions who did not receive an NASG.Methods: This observational study analyzed a historic cohort of 154 patients with PPH, secondary hypovolemic shock and signs of hypoperfusion who were admitted to this institution from 2012 to 2015. Group 1 (n= 77) was managed with NASG and Group 2 (n = 77) received interventions other than NASG. Hypoperfusion markers and maternal outcomes were compared in both groups.Results: Of 154 patients included in the analysis, 36.4% required a total abdominal hysterectomy (TAH) to achieve hemorrhage control, 98.2% of whom belonged to Group 2 and 1.8% to Group 1 (p = .001). The use of blood products was more common in Group 2 (p < .001), as was the administration of vasoactive agents. The mean number of days of hospitalization at the Obstetric High Dependency Unit (OHDU) was significantly lower in Group 1 and reached a statistically significant p value. Only two cases of maternal death occurred in Group 2.Discussion: The use of NASG in the management of PPH is a cost-effective strategy for patients with severe shock and signs of hypoperfusion and is optimal in a limited-resource scenario. In this study, the use of NASG was related to better outcomes in a statistically significant manner with better results regarding maternal outcomes such as uterine preservation and decreased transfusion requirements and hospital days.Conclusions: NASG, associated with the use of uterotonic agents and other strategies for PPH control, is a safe tool that helps reduce morbimortality in critically ill patients with PPH.


Subject(s)
Postpartum Hemorrhage , Shock , Blood Transfusion , Clothing , Female , Humans , Maternal Mortality , Postpartum Hemorrhage/therapy , Pregnancy , Shock/etiology , Shock/therapy
14.
Proteins ; 87(12): 1361-1377, 2019 12.
Article in English | MEDLINE | ID: mdl-31265154

ABSTRACT

Methods to reliably estimate the accuracy of 3D models of proteins are both a fundamental part of most protein folding pipelines and important for reliable identification of the best models when multiple pipelines are used. Here, we describe the progress made from CASP12 to CASP13 in the field of estimation of model accuracy (EMA) as seen from the progress of the most successful methods in CASP13. We show small but clear progress, that is, several methods perform better than the best methods from CASP12 when tested on CASP13 EMA targets. Some progress is driven by applying deep learning and residue-residue contacts to model accuracy prediction. We show that the best EMA methods select better models than the best servers in CASP13, but that there exists a great potential to improve this further. Also, according to the evaluation criteria based on local similarities, such as lDDT and CAD, it is now clear that single model accuracy methods perform relatively better than consensus-based methods.


Subject(s)
Computational Biology , Protein Conformation , Proteins/ultrastructure , Software , Algorithms , Databases, Protein , Models, Molecular , Protein Folding , Proteins/chemistry , Proteins/genetics , Sequence Alignment , Sequence Analysis, Protein
15.
Curr Protoc Bioinformatics ; 66(1): e75, 2019 06.
Article in English | MEDLINE | ID: mdl-31063641

ABSTRACT

In spite of the fact that there has been a significant increase in the number of solved protein structures, structural information is missing for many proteins. Although structural information is codified in the amino acid sequence, computational prediction using only this information is still an unsolved problem. However, one successful method to model a protein's structure starting from the primary sequence is to use contact prediction derived from multiple sequence alignment (MSA). Here we use our contact predictor PconsC4 to generate a list of probable contacts between residues in the primary sequences. These contacts are then used together with the secondary structure prediction as constraints for the CONFOLD folding method. In this way, a 3D protein model can be built starting directly from the primary sequence. © 2019 by John Wiley & Sons, Inc.


Subject(s)
Algorithms , Computational Biology/methods , Proteins/chemistry , Models, Molecular , Protein Structure, Secondary , Sequence Alignment
16.
Health Equity ; 3(1): 117-123, 2019.
Article in English | MEDLINE | ID: mdl-30989153

ABSTRACT

Purpose: Paid parental leave (PPL) policies offer immense opportunity to enhance health equity by providing financial stability to workers and promoting the health of families in the United States. Working in partnership with a local county government, which recently adopted a paid leave policy, we engaged in a qualitative substudy to enhance our understanding of how workers perceived and experienced the policy across levels of the socioecological framework. Methods: Working in partnership with Multnomah County, a large public-sector employer in Portland, OR that recently adopted a PPL policy, we collected qualitative data through focus groups with employees. Data were transcribed, coded, and analyzed thematically. Results: We conducted seven focus groups with county employees (N=35) in the fall of 2017. Three major themes emerged from the focus group data: intersectional inequities, disparities by department, and uneven benefits. Conclusions: Our findings highlight the inequities of experience with the PPL policy across employees at individual, organization, and environmental levels. These findings offer insight and guidance for entities considering the adoption and implementation of such policies to consider concrete steps to enhance equity of access and experience.

17.
J Mol Biol ; 431(13): 2442-2448, 2019 06 14.
Article in English | MEDLINE | ID: mdl-30796988

ABSTRACT

At present, about half of the protein domain families lack a structural representative. However, in the last decade, predicting contact maps and using these to model the tertiary structure for these protein families have become an alternative approach to gain structural insight. At present, reliable models for several hundreds of protein families have been created using this approach. To increase the use of this approach, we present PconsFam, which is an intuitive and interactive database for predicted contact maps and tertiary structure models of the entire Pfam database. By modeling all possible families, both with and without a representative structure, using the PconsFold2 pipeline, and running quality assessment estimator on the models, we predict an estimation for how confident the contact maps and structures are for each family.


Subject(s)
Computational Biology/methods , Databases, Protein , Proteins/chemistry , Models, Molecular , Multigene Family , Protein Structure, Tertiary , Sequence Alignment
18.
J Occup Health Psychol ; 24(1): 36-54, 2019 Feb.
Article in English | MEDLINE | ID: mdl-29215909

ABSTRACT

Although job stress models suggest that changing the work social environment to increase job resources improves psychological health, many intervention studies have weak designs and overlook influences of family caregiving demands. We tested the effects of an organizational intervention designed to increase supervisor social support for work and nonwork roles, and job control in a results-oriented work environment on the stress and psychological distress of health care employees who care for the elderly, while simultaneously considering their own family caregiving responsibilities. Using a group-randomized organizational field trial with an intent-to-treat design, 420 caregivers in 15 intervention extended-care nursing facilities were compared with 511 caregivers in 15 control facilities at 4 measurement times: preintervention and 6, 12, and 18 months. There were no main intervention effects showing improvements in stress and psychological distress when comparing intervention with control sites. Moderation analyses indicate that the intervention was more effective in reducing stress and psychological distress for caregivers who were also caring for other family members off the job (those with elders and those "sandwiched" with both child and elder caregiving responsibilities) compared with employees without caregiving demands. These findings extend previous studies by showing that the effect of organizational interventions designed to increase job resources to improve psychological health varies according to differences in nonwork caregiving demands. This research suggests that caregivers, especially those with "double-duty" elder caregiving at home and work and "triple-duty" responsibilities, including child care, may benefit from interventions designed to increase work-nonwork social support and job control. (PsycINFO Database Record (c) 2019 APA, all rights reserved).


Subject(s)
Caregivers/psychology , Family Health , Health Personnel/psychology , Health Promotion/methods , Stress, Psychological/prevention & control , Stress, Psychological/psychology , Adolescent , Adult , Aged , Child , Child Care/psychology , Female , Humans , Intention to Treat Analysis , Male , Middle Aged , New England , Nursing Homes , Occupational Health , Social Support , Surveys and Questionnaires , Workplace/psychology , Young Adult
19.
Bioinformatics ; 35(15): 2677-2679, 2019 08 01.
Article in English | MEDLINE | ID: mdl-30590407

ABSTRACT

MOTIVATION: Residue contact prediction was revolutionized recently by the introduction of direct coupling analysis (DCA). Further improvements, in particular for small families, have been obtained by the combination of DCA and deep learning methods. However, existing deep learning contact prediction methods often rely on a number of external programs and are therefore computationally expensive. RESULTS: Here, we introduce a novel contact predictor, PconsC4, which performs on par with state of the art methods. PconsC4 is heavily optimized, does not use any external programs and therefore is significantly faster and easier to use than other methods. AVAILABILITY AND IMPLEMENTATION: PconsC4 is freely available under the GPL license from https://github.com/ElofssonLab/PconsC4. Installation is easy using the pip command and works on any system with Python 3.5 or later and a GCC compiler. It does not require a GPU nor special hardware. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Subject(s)
Deep Learning , Software
20.
Proteins ; 86(6): 654-663, 2018 06.
Article in English | MEDLINE | ID: mdl-29524250

ABSTRACT

Protein modeling quality is an important part of protein structure prediction. We have for more than a decade developed a set of methods for this problem. We have used various types of description of the protein and different machine learning methodologies. However, common to all these methods has been the target function used for training. The target function in ProQ describes the local quality of a residue in a protein model. In all versions of ProQ the target function has been the S-score. However, other quality estimation functions also exist, which can be divided into superposition- and contact-based methods. The superposition-based methods, such as S-score, are based on a rigid body superposition of a protein model and the native structure, while the contact-based methods compare the local environment of each residue. Here, we examine the effects of retraining our latest predictor, ProQ3D, using identical inputs but different target functions. We find that the contact-based methods are easier to predict and that predictors trained on these measures provide some advantages when it comes to identifying the best model. One possible reason for this is that contact based methods are better at estimating the quality of multi-domain targets. However, training on the S-score gives the best correlation with the GDT_TS score, which is commonly used in CASP to score the global model quality. To take the advantage of both of these features we provide an updated version of ProQ3D that predicts local and global model quality estimates based on different quality estimates.


Subject(s)
Models, Molecular , Proteins/chemistry , Algorithms , Databases, Protein , Machine Learning , Protein Conformation , Software , Structure-Activity Relationship
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