Category: Nevin Manimala

J Anim Ecol. 2022 Mar 23. doi: 10.1111/1365-2656.13692. Online ahead of print.

ABSTRACT

Genetic adaptation to future environmental conditions is crucial to help species persist as the climate changes. Genome scans are powerful tools to understand adaptive landscapes, enabling us to correlate genetic diversity with environmental gradients while disentangling neutral from adaptive variation. However, low gene flow can lead to both local adaptation and highly structured populations, and is a major confounding factor for genome scans, resulting in an inflated number of candidate loci. Here, we compared candidate locus detection in a marine mollusc (Onithochiton neglectus), taking advantage of a natural geographic contrast in the levels of genetic structure between its populations. O. neglectus is endemic to New Zealand and distributed throughout an environmental gradient from the sub-tropical north to the subantarctic south. Due to a brooding developmental mode, populations tend to be locally isolated. However, adult hitchhiking on rafting kelp increases connectivity among southern populations. We applied two genome scans for outliers (Bayescan and PCAdapt) and two genotype-environment association (GEA) tests (BayeScEnv and RDA). To limit issues with false positives, we combined results using the geometric mean of q-values and performed association tests with random environmental variables. This novel approach is a compromise between stringent and relaxed approaches widely used before, and allowed us to classify candidate loci as low- or high-confidence. Genome scans for outliers detected a large number of significant outliers in strong and moderately structured populations. No high-confidence GEA loci were detected in the context of strong population structure. However, 86 high-confidence loci were associated predominantly with latitudinally-varying abiotic factors in the less structured southern populations. This suggests that the degree of connectivity driven by kelp-rafting over the southern scale may be insufficient to counteract local adaptation in this species. Our study supports the expectation that genome scans may be prone to errors in highly structured populations. Nonetheless, it also empirically demonstrates that careful statistical controls enable the identification of candidate loci that invite more detailed investigations. Ultimately, genome scans are valuable tools to help guide further research aiming to determine the potential of non-model species to adapt to future environments.

PMID:35318661 | DOI:10.1111/1365-2656.13692

J Forensic Sci. 2022 Mar 22. doi: 10.1111/1556-4029.15028. Online ahead of print.

ABSTRACT

The proceeding developments in next generation sequencing (NGS) technologies enable increasing discrimination power for short tandem repeat (STR) analyses and provide new possibilities for human identification. Therefore, the growing relevance and demand in forensic casework display the need for reliable validation studies and experiences with challenging DNA samples. The presented validation of the MiSeq FGx system and the ForenSeq™ DNA Signature Prep Kit (1) investigated sensitivity, repeatability, reproducibility, concordance, pooling variations, DNA extraction method variances, DNA mixtures, degraded, and casework samples and (2) optimized the sequencing workflow for challenging samples from human corpses by testing additional PCR purification, pooling adjustments, and adapter volume reductions. Overall results indicate the system’s reliability in concordance to traditional capillary electrophoresis (CE)-based genotyping and reproducibility of sequencing data. Genotyping success rates of 100% were obtained down to 62.5 pg DNA input concentrations. Autosomal STR (aSTR) profiles of artificially degraded samples revealed significantly lower numbers of locus and allelic dropouts than CE. However, it was observed that the system still exposed drawbacks when sequencing highly degraded and inhibited samples from human remains. Due to the lack of studies evaluating the sequencing success of samples from decomposed or skeletonised corpses, the presented optimisation studies provide valuable recommendations such as an additional PCR purification, an increase in library pooling volumes, and a reduction of adapter volumes for samples with concentrations ≥31.2 pg. Thus, this research highlights the importance of all-encompassing validation studies for implementing novel technologies in forensic casework and presents recommendations for challenging samples.

PMID:35318655 | DOI:10.1111/1556-4029.15028

Biometrics. 2022 Mar 22. doi: 10.1111/biom.13664. Online ahead of print.

ABSTRACT

Nonparametric feature selection for high-dimensional data is an important and challenging problem in the fields of statistics and machine learning. Most of the existing methods for feature selection focus on parametric or additive models which may suffer from model misspecification. In this paper, we propose a new framework to perform nonparametric feature selection for both regression and classification problems. Under this framework, we learn prediction functions through empirical risk minimization over a reproducing kernel Hilbert space (RKHS). The space is generated by a novel tensor product kernel which depends on a set of parameters that determines the importance of the features. Computationally, we minimize the empirical risk with a penalty to estimate the prediction and kernel parameters simultaneously. The solution can be obtained by iteratively solving convex optimization problems. We study the theoretical property of the kernel feature space and prove the oracle selection property and Fisher consistency of our proposed method. Finally, we demonstrate the superior performance of our approach compared to existing methods via extensive simulation studies and applications to two real studies. This article is protected by copyright. All rights reserved.

PMID:35318639 | DOI:10.1111/biom.13664

Int J Gynaecol Obstet. 2022 Mar 23. doi: 10.1002/ijgo.14136. Online ahead of print.

ABSTRACT

OBJECTIVE: To assess the effects of “sperm-friendly” coital lubricants on sperm motility.

METHODS: This study compared the effects of five lubricants (Optilube®, Pre-Seed®, Yes Baby®, olive oil, and egg white) on sperm motility in 60 normozoospermic semen samples obtained from men attending a private fertility clinic. Samples were exposed to each of the lubricants, with untreated samples serving as controls, and were examined microscopically at four defined time-points from 2 to 72 h after liquefaction. Sperm motility was graded according to World Health Organization criteria.

RESULTS: With the exception of egg white, all lubricants caused significant (P < 0.001) reductions in sperm forward progression compared with untreated controls until 24 h after liquefaction. Furthermore, between-group comparisons of the commercially available lubricants revealed statistically significant differences in forward progression motility: Pre-Seed® was superior to Optilube® (P < 0.001), which in turn was superior to Yes Baby® (P < 0.001) at 2-4 h after exposure. Significance (P < 0.001) between Pre-Seed® and Yes Baby® was maintained until 24 h.

CONCLUSION: Although spermatozoa exposed to Pre-Seed® demonstrated greater motility than spermatozoa exposed to Yes Baby®, claims that these lubricants are sperm-friendly were refuted. Conversely, egg white was shown to be a sperm-friendly lubricant for couples who are trying to conceive.

PMID:35318650 | DOI:10.1002/ijgo.14136

Hu Li Za Zhi. 2022 Apr;69(2):89-96. doi: 10.6224/JN.202204_69(2).11.

ABSTRACT

Societal ageing, the rising prevalence of chronic diseases, and the COVID-19 pandemic have changed the global healthcare environment dramatically. These challenges have significantly burdened community medical and healthcare systems and complicated the work of public health nursing. As an important care provider on the frontlines of primary care, public health nurses (PHNs) must keep up with the current state of the medical environment and statistical data interpretation, scientific data translation, community resource sharing, and telehealth applications. These demands have greatly impacted the traditional routines and existing professional core competencies of PHNs. Discussions among 12 Taiwanese public healthcare experts and the definition of public health nursing capacity from World Health Organization were considered in this review. In addition to reflecting on social changes and the professional development of public health nursing, eight prospective recommendations were provided in this review to enhance the professional competence of PHNs and better prepare them for future changes in the health environment and primary healthcare. The suggestions provide a reference for updating the position statement of PHNs.

PMID:35318636 | DOI:10.6224/JN.202204_69(2).11

Gesundheitswesen. 2022 Mar 22. doi: 10.1055/a-1749-5508. Online ahead of print.

ABSTRACT

AIM OF THE STUDY: The objective of this analysis was to record the social and epidemiological characteristics of a specific sample population, as well as to identify any associations between a previous commitment to a public facility on legal grounds and subsequent assessments of an individual’s fitness to drive as per the National Health Service (or “ÖGD”).

METHODS: For the retrospective data analysis, the documents of 87 subjects were evaluated who had been committed to public psychiatric institutions on legal grounds between 2015 and 2019. Using the SAS software package, frequency distributions and statistical relationships were identified between specific features of the commitment to accommodation and the assessment of fitness to drive by means of Chi-squared testing.

RESULTS: The average age of the study cohort was 43.5 years (range: 16-82 years; male: 59%). The most frequent grounds for commitment to a facility were suicidal intentions expressed by the person in question. In one third of the cases, these individuals were under the influence of alcohol at the time of commitment to the facility, and drug use was documented in 3 of the 87 cases. In 74% of cases, confinement was solely due to an individual’s risk to themselves; in 26% a risk to others was (additionally) identified; and in 20% of those affected, there was verbal and/or physical resistance to commitment to the accommodation facility. In 57% of cases, the medical evaluation raised doubts about the individual’s fitness to drive, resulting in the matter being referred on to the driving license authority. Statistically significant associations were demonstrated between: a) the grounds for commitment to a facility; the type of risk; and resistance to commitment being enforced, and b) the results of a fitness-to-drive assessment carried out by the ÖGD.

CONCLUSION: The data available on individuals committed to public facilities on legal grounds in connection with driving-related medical issues should be optimised to improve quality, whereby the anonymous registration system, introduced on the basis of the Bavarian Mental Health Act (“BayPsychoKHG”), can make a contribution in this regard. In addition, further qualification measures for effective quality management are necessary for all actors involved.

PMID:35318625 | DOI:10.1055/a-1749-5508

Behav Res Methods. 2022 Mar 22. doi: 10.3758/s13428-022-01811-w. Online ahead of print.

ABSTRACT

In conceptual properties norming studies (CPNs), participants list properties that describe a set of concepts. From CPNs, many different parameters are calculated, such as semantic richness. A generally overlooked issue is that those values are only point estimates of the true unknown population parameters. In the present work, we present an R package that allows us to treat those values as population parameter estimates. Relatedly, a general practice in CPNs is using an equal number of participants who list properties for each concept (i.e., standardizing sample size). As we illustrate through examples, this procedure has negative effects on data’s statistical analyses. Here, we argue that a better method is to standardize coverage (i.e., the proportion of sampled properties to the total number of properties that describe a concept), such that a similar coverage is achieved across concepts. When standardizing coverage rather than sample size, it is more likely that the set of concepts in a CPN all exhibit a similar representativeness. Moreover, by computing coverage the researcher can decide whether the CPN reached a sufficiently high coverage, so that its results might be generalizable to other studies. The R package we make available in the current work allows one to compute coverage and to estimate the necessary number of participants to reach a target coverage. We show this sampling procedure by using the R package on real and simulated CPN data.

PMID:35318591 | DOI:10.3758/s13428-022-01811-w

Mol Biol Rep. 2022 Mar 22. doi: 10.1007/s11033-022-07354-9. Online ahead of print.

ABSTRACT

Phosphorus (P), an essential nutrient required by plants often becomes the limiting factor for plant growth and development. Plants employ various mechanisms to sense the continuously changing P content in the soil. Transcription factors, such as SHORT ROOT (SHR), AUXIN RESPONSE FACTOR19 (ARF19), and ETHYLENE-INSENSITIVE3 (EIN3) regulate the growth of primary roots, root hairs, and lateral roots under low P. Crop improvement strategies under low P depend either on improving P acquisition efficiency or increasing P utilization. The various phosphate transporters (PTs) are involved in the uptake and transport of P from the soil to various plant cellular organelles. A plethora of regulatory elements including transcription factors, microRNAs and several proteins play a critical role in the regulation of coordinated cellular P homeostasis. Among these, the well-established P starvation signaling pathway comprising of central transcriptional factor phosphate starvation response (PHR), microRNA399 (miR399) as a long-distance signal molecule, and PHOSPHATE 2 (PHO2), an E2 ubiquitin conjugase is crucial in the regulation of phosphorus starvation responsive genes. Under PHR control, several classes of PHTs, microRNAs, and proteins modulate root architecture, and metabolic processes to enable plants to adapt to low P. Even though sucrose and inositol phosphates are known to influence the phosphorus starvation response genes, the exact mechanism of regulation is still unclear. In this review, a basic understanding of P homeostasis under low P in plants and all the above aspects are discussed.

PMID:35318578 | DOI:10.1007/s11033-022-07354-9

Zhonghua Zhong Liu Za Zhi. 2022 Mar 23;44(3):291-296. doi: 10.3760/cma.j.cn112152-20201014-00897.

ABSTRACT

Objective: To analyze the clinical efficacy of fertility-preserving therapy in patients with atypical endometrial hyperplasia (AEH) and early endometrial carcinoma (EC). Methods: The general condition, pathological type, treatment plan, tumor outcomes and pregnancy outcomes of 110 patients with AEH and EC treated with fertility-preserving therapy in Peking University People’s Hospital from December 2005 to September 2019 were retrospectively analyzed. Kaplan-Meier and Log rank tests were used for survival analysis. Results: The response rate of 110 cases of AEH (62 cases) and EC (48 cases) was 94.5% (104/110) after fertility-preserving therapy. There were 93 cases (84.5%) achieved complete response and 11 cases (10.0%) achieved partial response, and the recurrence rate was 29.0% (27/93). The complete response rates of AEH and EC were 90.3% (56/62) and 77.1% (37/48), respectively, without significant difference (P=0.057). The recurrence rates of EC were significantly higher than that of AEH (40.5% vs 21.4%; P=0.022). Forty-one patients with complete response had pregnancy intention, the pregnancy rate was 70.7% (29/41), and the live birth rate was 56.1% (23/41). The live birth rate of AEH was 68.2% (15/22) and that of EC was 42.1% (8/19), the difference was statistically significant (P=0.032). The pathological type was related with the recurrence (P=0.044). Conclusions: Patients with AEH and EC can obtain high complete response rate and pregnancy rate after fertility-preserving therapy. The recurrence rate of EC is higher than that of AEH, while the live birth rate of AEH is higher than that of EC.

PMID:35316880 | DOI:10.3760/cma.j.cn112152-20201014-00897

Zhonghua Zhong Liu Za Zhi. 2022 Mar 23;44(3):260-267. doi: 10.3760/cma.j.cn112152-20200803-00704.

ABSTRACT

Objective: To investigate the expression of programmed death ligand-1 (PD-L1, SP142) and PD-L1 (22C3) in triple-negative breast cancer (TNBC), and analyze their correlation with the clinicopathological factors and prognosis. Methods: The clinicopathologic data of 259 patients with TNBC treated in Cancer Hospital from August 2010 to December 2013 were collected. Whole section of surgical tissue samples were collected to conduct PD-L1 (SP142) and PD-L1 (22C3) immunohistochemical (IHC) staining. The PD-L1 expression in tumor cells and tumor infiltrating immune cells were visually assessed respectively, the relationship between PD-L1 expression and clinicopathologic characterizes were analyzed. Univariable and multivariable Cox proportional hazards regression models were used to test the correlations between PD-L1 expression and disease-free survival (DFS) and overall survival (OS). Results: The positive rates of SP142 (immune cell score, ICs≥1%) and 22C3 (combined positive score, CPS≥1) were 42.1%(109/259) and 41.3%(107/259) in TNBC tissues, respectively, with a total coincidence rate of 82.3%. The Kappa value of positive expression cases was 0.571 and the distribution difference of SP142 and 22C3 positive expression cases was statistically significant (P<0.001). The PD-L1 positive patients were less likely to have vascular invasion (P<0.05), but with higher histological grade and Ki-67 proliferation index (P<0.05). The recurrence/metastasis cases(8) of the patients with positive PD-L1 (SP142) was significantly lower than that of patients with negative PD-L1(SP142, 27, P=0.016). The positive expression of PD-L1 (SP142) patients were longer DFS (P=0.019). The OS of patients with positive PD-L1 (SP142) were longer than those with negative PD-L1 (SP142), but without significance (P=0.116). The positive expression of PD-L1 (22C3) was marginally associated with DFS and OS of patients (P>0.05). Conclusions: The expression of PD-L1 (22C3) is different from that of PD-L1 (SP142) in TNBC, and the two antibodies can’t be interchangeable for each other in clinical tests. PD-L1 (SP142) status is an independent prognostic factor of DFS in TNBC. The DFS is significantly prolonged in patients with positive expression of PD-L1 (SP142).

PMID:35316876 | DOI:10.3760/cma.j.cn112152-20200803-00704