Nevin Manimala

J Mol Biol. 2023 Aug 1;435(15):168181. doi: 10.1016/j.jmb.2023.168181. Epub 2023 Jun 9.

ABSTRACT

Identifying the common structural elements of functionally related RNA sequences (family) is usually based on an alignment of the sequences, which is often subject to human bias and may not be accurate. The resulting covariance model (CM) provides probabilities for each base to covary with another, which allows to support evolutionarily the formation of double helical regions and possibly pseudoknots. The coexistence of alternative folds in RNA, resulting from its dynamic nature, may lead to the potential omission of motifs by CM. To overcome this limitation, we present D-ORB, a system of algorithms that identifies overrepresented motifs in the secondary conformational landscapes of a family when compared to those of unrelated sequences. The algorithms are bundled into an easy-to-use website allowing users to submit a family, and optionally provide unrelated sequences. D-ORB produces a non-pseudoknotted secondary structure based on the overrepresented motifs, a deep neural network classifier and two decision trees. When used to model an Rfam family, D-ORB fits overrepresented motifs in the corresponding Rfam structure; more than a hundred Rfam families have been modeled. The statistical approach behind D-ORB derives the structural composition of an RNA family, making it a valuable tool for analyzing and modeling it. Its easy-to-use interface and advanced algorithms make it an essential resource for researchers studying RNA structure. D-ORB is available at https://d-orb.major.iric.ca/.

PMID:37468182 | DOI:10.1016/j.jmb.2023.168181

BMJ. 2023 Jul 19;382:e071757. doi: 10.1136/bmj-2022-071757.

NO ABSTRACT

PMID:37468141 | DOI:10.1136/bmj-2022-071757

Can J Cardiol. 2023 Jul 17:S0828-282X(23)01521-0. doi: 10.1016/j.cjca.2023.07.014. Online ahead of print.

ABSTRACT

The Cox proportional hazards model is one of the most popular statistical tools to model time to event outcomes without the need for specifying the hazards or survival time distributions. The Cox model requires that the ratio of the hazards of the occurrence of the outcome for any two individuals remain constant during the entire follow-up. Studies comparing coronary revascularization strategies, however, might be prone to violations of proportionality by the crossing of the hazard functions over time. Early increases in the risk of cardiovascular outcomes are commonly observed when comparing coronary artery bypass grafting versus percutaneous coronary intervention, while decreased risk might be observed later during the follow-up. The same is valid for comparisons between invasive versus conservative coronary revascularization strategies. In these situations, the statistical power of the Cox model is reduced, and hazard ratios might not be an informative summary measure of treatment effect. In this manuscript, we discuss methods to identify and account for nonproportionality. We illustrate the use of these methods in a case study, based on reconstructed data from a coronary revascularization clinical trial. Finally, we review the cardiovascular literature to estimate how the proportionality assumption has been reported in coronary revascularization studies recently.

PMID:37468120 | DOI:10.1016/j.cjca.2023.07.014

Am J Ophthalmol. 2023 Jul 17:S0002-9394(23)00288-X. doi: 10.1016/j.ajo.2023.07.010. Online ahead of print.

ABSTRACT

PURPOSE: Ultra-widefield (UWF) imaging is commonly used in ophthalmology in tandem with scleral depressed examinations (SDE) to evaluate peripheral retinal disease. Due to increased reliance of this technology in tele-ophthalmology, it is critical to evaluate its efficacy for detecting the peripheral retina when performed in isolation. Therefore, we sought to evaluate UWF imaging sensitivity in detecting retinal horseshoe tears (HST).

DESIGN: A retrospective clinical validity and reliability study METHODS: A single-institutional retrospective analysis was performed on patients at the Shiley Eye Institute, UC, San Diego. Those with HSTs seen on SDE and underwent treatment with laser were included in the study. 140 patients with HSTs in the right and/or left eyes met the inclusion criteria. Those with concomitant ruptured globes, retinal detachments and vitreous hemorrhages were excluded. A total of 123 patients with 135 HSTs were included in the final analysis. The primary outcome was the number of HSTs detected by UWF imaging. A secondary outcome was HST location. Sensitivity was measured with respect to HST location and statistical significance was calculated by Fisher exact testing.

RESULTS: 69 (51.1%) HSTs were visualized on UWF images and 66 (48.9%) were not visualized. The sensitivity of UWF imaging in capturing HSTs was 7/41 (17.1%), 8/25 (32.0%), 7/14 (50.0%) and 47/55 (85.5%) for the superior, inferior, nasal and temporal quadrants, respectively. Sensitivities among HST visibility and location were statistically significant (p < 0.001) CONCLUSIONS: Nearly half of HSTs were missed by UWF imaging. This study demonstrates that UWF imagin.

PMID:37468086 | DOI:10.1016/j.ajo.2023.07.010

Prev Med. 2023 Jul 17:107624. doi: 10.1016/j.ypmed.2023.107624. Online ahead of print.

ABSTRACT

This paper tried to observe the relationship between the personality of patients with different personalities and the survival rate of replantation of traumatic amputated finger, and analyzed the influencing factors. EPQ psychological quality scores of patients with different gender, average monthly family income and age were significantly different (P < 0.05). In terms of the internal and external tendency score of EPQ, there were statistical requirements for differences in the mean monthly income of patients from different families (P < 0.05). For the concealment degree of EPQ, there were statistical requirements for differences in gender, family income, education level and patient scores (P < 0.05). In terms of mental state, the scores were higher than the standard, whether from the perspective of obsessive-compulsive symptoms, or from the perspective of interpersonal sensitivity, hostility, paranoia and other dimensions, the difference was statistically significant (P < 0.05). Patients with different personality types have different psychological problems after accidental amputation and replantation, which is directly related to the survival rate of postoperative finger amputation. Therefore, in order to effectively improve the survival rate of patients with finger amputation, the psychological condition of patients can be assessed, early detection and intervention of patients’ psychological problems, and appropriate intervention measures can be taken according to the personality characteristics of patients.

PMID:37468075 | DOI:10.1016/j.ypmed.2023.107624

J Acad Nutr Diet. 2023 Jul 17:S2212-2672(23)01275-3. doi: 10.1016/j.jand.2023.07.008. Online ahead of print.

ABSTRACT

BACKGROUND: Fiber intake may lower digestive tract cancer risk, possibly by modulating the composition of gut microbiota. However, no data is available about the role of specific fiber fractions with prebiotic activity, e.g., inulin-type fructans (ITFs), fructo-oligosaccharides (FOSs) and galactooligosaccharides (GOSs), on the risk lower digestive tract cancer.

OBJECTIVE: The objective was to assess the association between prebiotic intake and the risk of cancers of the upper digestive tract and stomach.

DESIGN: Within the PrebiotiCa study, data were derived from a network of Italian case-control studies conducted between 1992 and 2009. Participants’ usual diet was assessed using a food frequency questionnaire (FFQ). ITFs, and selected FOSs (nystose, kestose and 1F-β-fructofuranosylnystose) and GOSs (raffinose and stachyose) were quantified in several food products via laboratory analyses. Participants’ prebiotic intake was calculated by multiplying FFQ intake by the prebiotic content of each food item.

PARTICIPANTS/SETTING: Cases were patients admitted to major hospitals with incident histologically confirmed cancers; there were 946 cases of cancer of the oral cavity/pharynx, 198 of the nasopharynx, 304 of the esophagus, 230 of the stomach. Over 4,000 patients admitted to the same hospitals for acute non-neoplastic nor diet-related conditions were selected as controls.

MAIN OUTCOME MEASURES: The outcomes were oral and pharyngeal, nasopharyngeal, esophageal and stomach cancers.

STATISTICAL ANALYSES PERFORMED: The odds ratios (OR) and corresponding confidence intervals (CI) of the various cancers were derived using logistic regression models adjusted for major confounders and energy intake.

RESULTS: No association was observed between the intake of prebiotics and the risk of cancers of the oral cavity and pharynx, nasopharynx and esophagus. High raffinose intake reduced stomach cancer risk (OR for the third versus the first tertile 0.6, 95% confidence interval, CI: 0.3-0.9); no other prebiotic was associated with stomach cancer.

CONCLUSIONS: The current study does not support a major role of prebiotic fibers on selected upper digestive tract cancers. The association between high raffinose intake and reduced stomach cancer risk needs further investigation in future studies.

PMID:37468063 | DOI:10.1016/j.jand.2023.07.008

J Invest Dermatol. 2023 Jul 17:S0022-202X(23)02419-3. doi: 10.1016/j.jid.2023.04.036. Online ahead of print.

NO ABSTRACT

PMID:37468035 | DOI:10.1016/j.jid.2023.04.036

J Pain. 2023 Jul 17:S1526-5900(23)00475-3. doi: 10.1016/j.jpain.2023.07.009. Online ahead of print.

ABSTRACT

This study investigated for the first time the effects of individual and combined application of three learning techniques (verbal suggestions, classical conditioning, and observational learning) on placebo analgesia and extinction. Healthy participants (N = 206) were assigned to eight different groups in which they were taught through either a verbal suggestion, a conditioning paradigm, a video observing someone, or any combination thereof that a placebo device (inactive TENS) was capable of alleviating heat pain, whereas one group did not (control). Placebo analgesia was quantified as the within-group difference in experienced pain when the placebo device was (sham) ‘activated’ or ‘inactivated’ during equal pain stimuli, and compared between groups. Placebo analgesia was induced in groups with two or three learning techniques. Significantly stronger placebo analgesia was induced in the combination of all three learning techniques as compared to the individual learning techniques or control condition, underlining the additional contribution of 3 combined techniques. Extinction did not differ between groups. Furthermore, pain expectancies, but not state anxiety or trust, mediated placebo analgesia. Our findings emphasize the added value of combining 3 learning techniques to optimally shape expectancies that lead to placebo analgesia, which can be used in experimental and clinical settings. PERSPECTIVE: This unique experimental study compared the individual versus combined effects of three important ways of learning (verbal suggestions, classical conditioning, and observational learning) on expectation-based pain relief. The findings indicate that placebo effects occurring in clinical practice could be optimally strengthened if healthcare providers apply these techniques in combination.

PMID:37468025 | DOI:10.1016/j.jpain.2023.07.009

Sci Total Environ. 2023 Jul 17:165600. doi: 10.1016/j.scitotenv.2023.165600. Online ahead of print.

ABSTRACT

Armed conflicts have detrimental impacts on the environment, including land systems. The prevailing understanding of the relation between Land Use/Land Cover (LULC) and armed conflict fails to fully recognize the complexity of their dynamics – a shortcoming that could undermine food security and sustainable land/water resources management in conflict settings. The Syrian portion of the transboundary Orontes River Basin (ORB) has been a site of violent conflict since 2013. Correspondingly, the Lebanese and Turkish portions of the ORB have seen large influxes of refugees. A major challenge in any geoscientific investigation in this region, specifically the Syrian portion, is the unavailability of directly-measured “ground truth” data. To circumvent this problem, we develop a novel methodology that combines remote sensing products, machine learning techniques and quasi-experimental statistical analysis to better understand LULC changes in the ORB between 2004 and 2022. Through analysis of the resulting annual LULC maps, we can draw several quantitative conclusions. Cropland areas decreased by 21-24 % in Syria’s conflict hotspot zones after 2013, whereas a 3.4-fold increase was detected in Lebanon. The development of refugee settlements was also tracked in Lebanon and on the Syrian/Turkish borders, revealing different LULC patterns that depend on settlement dynamics. The results highlight the importance of understanding the heterogenous spatio-temporal LULC changes in conflict-affected and refugee-hosting countries. The developed methodology is a flexible, cloud-based approach that can be applied to wide variety of LULC investigations related to conflict, policy and climate.

PMID:37467974 | DOI:10.1016/j.scitotenv.2023.165600

Biomed J. 2023 Jul 17:100632. doi: 10.1016/j.bj.2023.100632. Online ahead of print.

ABSTRACT

BACKGROUND: Biomarker dynamics in different time-courses might be the primary reason why a static measurement of a single biomarker cannot accurately predict sepsis outcomes. Therefore, we conducted this prospective hospital-based cohort study to simultaneously evaluate the performance of several conventional and novel biomarkers of sepsis in predicting sepsis-associated mortality on different days of illness among patients with suspected sepsis.

METHODS: We evaluated the performance of 15 novel biomarkers including angiopoietin-2, pentraxin 3, sTREM-1, ICAM-1, VCAM-1, sCD14 and 163, E-selectin, P-selectin, TNF-alpha, interferon-gamma, CD64, IL-6, 8, and 10, along with few conventional markers for predicting sepsis-associated mortality. Patients were grouped into quartiles according to the number of days since symptom onset. Receiver operating characteristic curve (ROC) analysis was used to evaluate the biomarker performance.

RESULTS: From 2014 to 2017, 1,483 patients were enrolled, of which 78% fulfilled the systemic inflammatory response syndrome criteria, 62% fulfilled the sepsis-3 criteria, 32% had septic shock, and 3.3% developed sepsis-associated mortality. IL-6, pentraxin 3, sCD163, and the blood gas profile demonstrated better performance in the early days of illness, both before and after adjusting for potential confounders (adjusted area under ROC curve [AUROC]:0.81-0.88). Notably, the Sequential Organ Failure Assessment (SOFA) score was relatively consistent throughout the course of illness (adjusted AUROC:0.70-0.91).

CONCLUSION: IL-6, pentraxin 3, sCD163, and the blood gas profile showed excellent predictive accuracy in the early days of illness. The SOFA score was consistently predictive of sepsis-associated mortality throughout the course of illness, with an acceptable performance.

PMID:37467969 | DOI:10.1016/j.bj.2023.100632