Hydrophobic forces and the length limit of foldable protein domains

To find the native conformation (fold), proteins sample a subspace that is typically hundreds of orders of magnitude smaller than their full conformational space. Whether such fast folding is intrinsic or the result of natural selection, and what is the longest foldable protein, are open questions. Here, we derive the average conformational degeneracy of a lattice polypeptide chain in water and quantitatively show that the constraints associated with hydrophobic forces are themselves sufficient to reduce the effective conformational space to a size compatible with the folding of proteins up to approximately 200 amino acids long within a biologically reasonable amount of time. This size range is in general agreement with the experimental protein domain length distribution obtained from approximately 1,200 proteins. Molecular dynamics simulations of the Trp-cage protein confirm this picture on the free energy landscape. Our analytical and computational results are consistent with a model in which the length and time scales of protein folding, as well as the modular nature of large proteins, are dictated primarily by inherent physical forces, whereas natural selection determines the native state.     

The minimal important difference in the 6-minute walk test for patients with pulmonary arterial hypertension

Rationale: Although commonly used as the primary outcome measure of clinical trials in pulmonary arterial hypertension (PAH), the minimal important difference (MID) of the 6-minute walk test (6MWT) has not been well defined for this population of patients. Objectives: To estimate the MID in the 6MWT in patients with PAH. Methods: Study subjects from the clinical trial of tadalafil in PAH, a 16-week, parallel-group, randomized clinical trial of patients who were treatment naive or on background therapy with an endothelin receptor antagonist, were eligible. 6MWT was performed using a standardized protocol. Distributional and anchor-based methods were used to estimate the MID; the latter method used the Physical Component Summary Score (PCS) of the Medical Outcomes Study 36-item short form (SF-36). Measurements and Main Results: Four hundred five subjects were analyzed. Domains of the SF-36 were weakly to modestly associated with 6MWT. Change in the PCS of the SF-36 was most strongly associated with change in 6MWT (r = 0.40, P < 0.001) and thus was selected as the anchor for subsequent anchor-based analyses. Distributional analyses yielded estimates of the MID ranging from 25.1 to 38.5 m, whereas anchor-based analyses yielded an estimate of 38.6 m. Conclusions: Using both distributional and anchor-based methods, the estimated consensus MID in the 6MWT for PAH is approximately 33 m. These results have important implications for (1) assessing treatment responses from clinical trials and metaanalyses of specific PAH therapy, and (2) sample size calculations for future study design.     

Prevalence and Factors Associated with Depression,Anxiety and Stress in IBD Patients Undergoing Intravenous Biological Therapy during the COVID-19 Pandemic-Montenegro Experience

Throughout its duration, the coronavirus disease 2019 (COVID-19) pandemic has been affecting lives worldwide and has had a sizeable impact on mental health, particularly for those who already suffer from a chronic illnesses. Depression, Anxiety and Stress (DAS) are common psychiatric comorbidities in inflammatory bowel disease (IBD) patients. This study aims to determine the prevalence and risk factors for moderate and severe symptoms of DAS in IBD patients have been undergoing intravenous biological therapy (IvBTh) during the COVID-19 pandemic. The study was conducted between September 1^st and November 30^th, 2020 at the Clinical Center of Montenegro-IBD unit, where all patients from Montenegro received the registered IvBTh. This case control study consists of 94 IBD patients that completed a validated questionnaire Depression, Anxiety and Stress Score-21 (DASS-21). A total of 59 patients received tumor necrosis factor alpha inhibitors (anti-TNF therapy), while 35 received anti-integrin therapy. After we calculated the DASS-21 score, we divided the patients into two groups: those who had moderate and severe symptoms (if they had any of the mentioned DASS-21 subscale score above limit for moderate or more severe symptoms: DASS-21 Depression, higher than 14; DASS-21 Anxiety, higher than 10 and DASS-21 Stress, higher than 19) and those who did not have significant symptoms (DASS-21 subscale score did not exceed the limit). We also examined demographic data, data on IBD characteristics and COVID-19 data and their impact on mental disorders. Standard statistical processing tests were used to identify risk factors for examined mental disorders. Following the DASS-21 criteria, we diagnosed the least moderate depression in 19.1%, anxiety in 14.9% and stress in 20.2% patients. The multivariate analysis indicated there to be a statistically significant relation of being higher at risk of developing depression, anxiety and stress when suffering from an active form of IBD (OR 6.487; 95% Cl 1.220–34.500, P = 0.028). Almost one third (30.9%) of patients have at least one of the examined mental disorders during the COVID-19 pandemic. Particular attention and efforts must be better focused on patients who suffer from an active form of IBD during the ongoing COVID-19 pandemic.     

Measurement properties and interpretability of the Chronic respiratory disease questionnaire (CRQ)

The chronic respiratory questionnaire, available as an interviewer and a self-administered instrument, includes 20 items across four domains: dyspnea (5 items), fatigue (4 items), emotional function (7 items), and mastery (4 items). When completing this instrument, patients rate their experience on a 7-point scale ranging from 1 (maximum impairment) to 7 (no impairment). The Chronic Respiratory Questionnaire has demonstrated excellent measurement properties for both discriminative and evaluative purposes and served as a model in numerous methodological studies in chronic airflow limitation and patients with chronic obstructive pulmonary disease. We performed a systematic review of the literature on the chronic respiratory questionnaire to summarize the key qualities of the chronic respiratory questionnaire and to appraise the work regarding the minimal important difference of the chronic respiratory questionnaire. This paper includes a revision of our initial definition of the minimal important difference and a methodological framework for using anchor based approaches to establish the minimal important difference pioneered by Jaeschke and colleagues. Other approaches to evaluate the minimal important difference include distribution-based methods and panel-based methods. Investigators have used all of these approaches to establish the minimal important difference for the chronic respiratory questionnaire and the results are in general agreement with the minimal important difference of 0.5 for the mean domain scores of the chronic respiratory questionnaire. As a result of this literature review and discussion at the workshop, we established several research objectives. These objectives include the exploration of presentation of quality of life information and prospective anchor-based approaches.     

Multimorbidity and Evidence Generation

Most people with a chronic disease actually have more than one, a condition known as multimorbidity. Despite this, the evidence base to prevent adverse disease outcomes has taken a disease-specific approach. Drawing on a conference, Improving Guidelines for Multimorbid Patients, the goal of this paper is to identify challenges to the generation of evidence to support the care of people with multimorbidity and to make recommendations for improvement. We identified three broad categories of challenges: 1) challenges to defining and measuring multimorbidity; 2) challenges related to the effects of multimorbidity on study design, implementation and analysis; and 3) challenges inherent in studying heterogeneity of treatment effects in patients with differing comorbid conditions. We propose a set of recommendations for consideration by investigators and others (reviewers, editors, funding agencies, policymaking organizations) involved in the creation of evidence for this common type of person that address each of these challenges. The recommendations reflect a general approach that emphasizes broader inclusion (recruitment and retention) of patients with multimorbidity, coupled with more rigorous efforts to measure comorbidity and comorbidity burden and the influence of multimorbidity on outcomes and the effects of therapy. More rigorous examination of heterogeneity of treatment effects requires careful attention to prioritizing the most important comorbid-related questions, and also requires studies that provide greater statistical power than conventional trials have provided. Relatively modest changes in the orientation of current research along these lines can be helpful in pointing to and partially addressing selected knowledge gaps. However, producing a robust evidence base to support patient-centered decision making in complex individuals with multimorbidity, exposed to many different combinations of potentially interacting factors that can modify the risks and benefits of therapies, is likely to require a clinical research enterprise fundamentally restructured to be more fully integrated with routine clinical practice.     

Incorporating genetics services into adult kidney disease care

Studies have shown that as many as 1 in 10 adults with chronic kidney disease has a monogenic form of disease. However, genetic services in adult nephrology are limited. An adult Kidney Genetics Clinic was established within the nephrology division at a large urban academic medical center to increase access to genetic services and testing in adults with kidney disease. Between June 2019 and December 2021, a total of 363 patients were referred to the adult Kidney Genetics Clinic. Of those who completed genetic testing, a positive diagnostic finding was identified in 27.1%, a candidate diagnostic finding was identified in 6.7% of patients, and a nondiagnostic positive finding was identified in an additional 8.6% of patients, resulting in an overall yield of 42.4% for clinically relevant genetic findings in tested patients. A genetic diagnosis had implications for medical management, family member testing, and eligibility for clinical trials. With the utilization of telemedicine, genetic services reached a diverse geographic and patient population. Genetic education efforts were integral to the clinic's success, as they increased visibility and helped providers identify appropriate referrals. Ongoing access to genomic services will remain a fundamental component of patient care in adults with kidney disease.