Evaluation and monitoring of the water quality of an Argentinian urban river applying multivariate statistics.

In this work, we present the water quality assessment of an urban river, the San Luis River, located in San Luis Province, Argentina. The San Luis River flows through two developing cities; hence, urban anthropic activities affect its water quality. The river was sampled spatially and temporally, evaluating ten physicochemical variables on each water sample. These data were used to calculate a Simplified Index of Water Quality in order to estimate river water quality and infer possible contamination sources. Data were statistically analyzed with the opensource software R, 4.1.0 version. Principal component analysis, cluster analysis, correlation matrices, and heatmap analysis were performed. Results indicated that water quality decreases in areas where anthropogenic activities take place. Robust inferential statistical analysis was performed, employing an alternative of multivariate analysis of variance (MANOVA), MANOVA.wide function. The most statistically relevant physicochemical variables associated with water quality decrease were used to develop a multiple linear regression model to estimate organic matter, reducing the variables necessary for continuous monitoring of the river and, hence, reducing costs. Given the limited information available in the region about the characteristics and recovery of this specific river category, the model developed is of vital importance since it can quickly detect anthropic alterations and contribute to the environmental management of the rivers. This model was also used to estimate organic matter at sites located in other similar rivers, obtaining satisfactory results.

Unsatisfactory Fecal Immunochemical Tests for Colorectal Cancer Screening: Prevalence, Reasons, and Subsequent Testing.

BACKGROUND: Fecal immunochemical test (FIT) is an effective colorectal cancer screening modality. Little is known about prevalence, reasons, and testing after unsatisfactory FIT, or a FIT that cannot be processed by the laboratory due to inadequate stool specimen or incomplete labeling. METHODS: Our retrospective cohort study examined unsatisfactory FIT among average-risk individuals aged 50-74 years in a large, integrated, safety-net health system who completed an index FIT from 2010 to 2019. We determined prevalence of unsatisfactory FIT and categorized reasons hierarchically. We used multivariable logistic regression models to identify factors associated with: (i) unsatisfactory FIT; and (ii) subsequent testing within 15 months of the unsatisfactory FIT. RESULTS: Of 56,980 individuals completing an index FIT, 10.2% had an unsatisfactory FIT. Reasons included inadequate specimen (51%), incomplete labeling (27%), old specimen (13%), and broken/leaking container (8%). Unsatisfactory FIT was associated with being male [OR, 1.10; confidence interval (CI), 1.03-1.16], Black (OR, 1.46; CI, 1.33-1.61), Spanish speaking (OR, 1.12; CI, 1.01-1.24), on Medicaid (OR, 1.42; CI, 1.28-1.58), and received FIT by mail (OR, 2.66; CI, 2.35-3.01). Among those with an unsatisfactory FIT, fewer than half (41%) completed a subsequent test within 15 months (median, 4.4 months). Adults aged 50-54 years (OR, 1.16; CI, 1.01-1.39) and those who received FIT by mail (OR, 1.92; CI, 1.49-2.09) were more likely to complete a subsequent test. CONCLUSIONS: One in ten returned a FIT that could not be processed, mostly due to patient-related reasons. Fewer than half completed a subsequent test after unsatisfactory FIT. IMPACT: Screening programs should address these breakdowns such as specimen collection and labeling to improve real-world effectiveness. See related In the Spotlight, p. 183.

Improving Colorectal Cancer Screening in a Regional Safety-Net Health System over a 10-Year Period: Lessons for Population Health.

BACKGROUND: Despite national policy efforts to increase colorectal cancer (CRC) screening, rates in vulnerable populations remain suboptimal. Many types of interventions have been employed, but their impact on improving population-level rates of CRC screening over time is uncertain. OBJECTIVE: Assess the impact of 10 years of different in-reach and outreach strategies to improve CRC screening and identify factors associated with being screen up-to-date (SUTD). DESIGN: Observational cohort study. PARTICIPANTS: Patients aged 50-74 years from 12 community-based primary care clinics in an integrated, regional safety-net health system. INTERVENTIONS: Multiple system-level interventions were implemented over time (visit-based electronic health record [EHR] reminders, quality measurement, annual preventive service letters, and mailed fecal immunohistochemical stool tests [FIT]). MAIN MEASURES: CRC SUTD rates by calendar year among those with a primary care (PC) visit in the prior 1 and 3 years and their multivariable correlates. KEY RESULTS: The sample included 31,786-40,405 patients/year. In 2011, mean age was 58.9, 63.9% were women, 37.0% were Hispanic, 39.3% Black, 16.8% White, and 6.6% Asian/Other, and 60.5% were uninsured/Medicaid. Three-quarters of patients had ≥ 1 PC visit in the prior year. Lower-intensity interventions (EHR reminders, quality measurement, annual prevention letters) had limited impact on SUTD rates (2-3% rise). Implementing system-wide mailed FIT increased rates from 51.2 to 61.9% among those with a PC visit in the past year (40.5 to 46.8% with a PC visit ≤ 3 years). Stopping mailed FIT due to COVID wiped out these gains. Higher screening rates were associated with the following: older age; female; more comorbidities, PC clinic visits, and prior FITs; and better insurance coverage. Hispanics had the highest SUTD rates followed by Asians, Blacks, and Whites (p < 0.05). CONCLUSIONS: Implementation of a system-wide mailed FIT program had the greatest impact on SUTD rates. Lower-intensity interventions (EHR reminders, quality measurement, and patient letters) had limited effects.

Intraoperative cytology when cryostat is not available. A 7-year experience in a Peruvian cancer center.

BACKGROUND: Intraoperative cytology (IC) is an alternative to frozen-section (FS) diagnosis. We present our experience with and the diagnostic value of IC during a 7-year period when FS was not available in a Peruvian Cancer Center. MATERIAL AND METHODS: This 7-year retrospective single-arm review study includes IC procedures performed by three pathologists between 2012 and 2018. These IC reports were reviewed independently by one pathologist and were correlated with the histologic diagnoses, which were used as the gold standard. All IC preparations (imprint, scrape, and crush smears) were stained with hematoxylin and eosin. IC interpretations were categorized as: malignant, benign, atypical, and "deferred to permanent sections." Sensitivity, specificity, and positive and negative predictive values were calculated by use of standard methods. RESULTS: A total of 1814 IC cases prepared from various organs obtained from 887 patients were reviewed. Malignant, benign, atypical, and "deferred to permanent sections" IC diagnoses were 26.3%, 68.9%, 3.7%, and 1.9%, respectively. Atypical and deferred cases were excluded from the statistical analysis; thus 1712 cases were found to be eligible. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and overall diagnostic accuracy were 91.6%, 97.7%, 94.1%, 96.7%, and 96%, respectively. CONCLUSION: In experienced hands, IC is a rapid, cost-effective, and accurate alternative diagnostic modality for intraoperative diagnosis when FS is not available.

Special considerations for evaluating psilocybin-facilitated psychotherapy in vulnerable populations.

Psilocybin-facilitated psychotherapy shows potential transdiagnostic efficacy for a range of mental health conditions. Though vulnerable populations bear disproportionate mental health burden, they have been largely neglected in the clinical psilocybin literature. However, if the field is to best respond to the diverse needs of individuals from vulnerable populations, care must be taken to ensure these individuals are represented in the empirical research. This report calls attention to this concern by detailing the challenges and opportunities associated with evaluating psilocybin-facilitated psychotherapy in vulnerable populations. First, we show how working with vulnerable populations must be considered in the context of an often-problematic past and differential exposure to and experience with classic psychedelics. We then provide actionable recommendations for future research testing psilocybin-facilitated psychotherapy in vulnerable populations, including an emphasis on recruitment strategies, the appropriate communication and assessment of subjective effects, building therapeutic alliance, multicultural competence, and flexible study designs. On these premises we call for future work in this area, underscoring that there is vast room for improvement and expansion in this rapidly advancing field of study.

Depression and Anxiety Are Common Among Patients With Cirrhosis.

BACKGROUND & AIMS: Depression and anxiety can have negative effects on patients and are important to treat. There have been few studies of their prevalence among patients with cirrhosis. We aimed to characterize the prevalence and risk factors for depression and anxiety in a large multi-center cohort of patients with cirrhosis. METHODS: We conducted a telephone-based survey of patients with cirrhosis at 3 health systems in the United States (a tertiary-care referral center, a safety net system, and a Veterans hospital) from April through December 2018. Of 2871 patients approached, 1021 (35.6%) completed the survey. Depression and anxiety were assessed using the PHQ-9 (range 0-25) and STAI (range 20-80) instruments, with clinically significant values defined as PHQ-9 ≥15 and STAI ≥40. We performed multivariate logistic regression analysis to identify factors associated with significant depression and anxiety. RESULTS: The median PHQ-9 score was 7 (25th percentile-75th percentile, 3-12) and the median STAI score was 33 (25th percentile-75th percentile, 23-47); 15.6% of patients had moderately severe to severe depression and 42.6% of patients had high anxiety. In multivariable analyses, self-reported poor health (odds ratio [OR], 4.08; 95% CI, 1.79-9.28), being widowed (OR, 2.08; 95% CI, 1.07-4.05), fear of hepatocellular carcinoma (OR, 1.89; 95% CI, 1.04-3.42), higher household income (OR, 0.30; 95% CI, 0.10-0.95), and Hispanic ethnicity (OR, 0.57; 95% CI, 0.33-0.97) were associated with moderately severe to severe depression. Male sex (OR, 0.71; 95% CI, 0.51-0.98), self-reported poor health (OR, 2.73; 95% CI, 1.73-4.32), and fear of hepatocellular carcinoma (OR, 2.24; 95% CI, 1.33-3.78) were associated with high anxiety. CONCLUSIONS: Nearly 1 in 6 patients with cirrhosis have moderately severe to severe depression and nearly half have moderate-severe anxiety. Patients with cirrhosis should be evaluated for both of these disorders.

Anal Cancer and Anal Cancer Screening Knowledge, Attitudes, and Perceived Risk Among Women Living With HIV.

OBJECTIVES: The aims of the study were (1) to describe anal cancer knowledge, perceived risk, screening barriers, and acceptability of sample self-collection among women living with HIV (WLWH) at an integrated safety-net system and (2) to describe differences in demographic and psychosocial variables among a subsample of WLWH with a history of abnormal cervical cytology results versus those with normal results. MATERIALS AND METHODS: We conducted telephone surveys with English- and Spanish-speaking WLWH (N = 99) and used electronic health record data to extract insurance type, CD4+ cell count, RNA viral load, and cervical cytology results. We calculated descriptive statistics for participant demographics, HIV laboratory results, and psychosocial variables. Among the subsample of women who completed a recent cervical Pap, we used Fisher exact test to assess differences in demographic variables, CD4+ counts, RNA viral loads, knowledge, awareness, acceptability, and perceived risk by cervical cytology results. RESULTS: Most participants (70%) reported knowing nothing about anal cancer; 28% correctly responded that HIV increases one's chance of getting anal cancer. Most (68%) never heard of an anal Pap test. Forty percent would get an anal Pap if they could self-collect the sample, whereas 59% were neutral or disagreed. The 2 most commonly cited barriers to obtaining an anal Pap were "I do not know enough about it" (n = 15) and "It might hurt" (n = 9). CONCLUSIONS: This study highlights a gap in knowledge and awareness among WLWH regarding their heightened risk for anal cancer. It indicates the need for health education and suggests an opportunity for a self-collection intervention.

GWAS to Identify Genetic Loci for Resistance to Yellow Rust in Wheat Pre-Breeding Lines Derived From Diverse Exotic Crosses.

Yellow rust (YR) or stripe rust, caused by Puccinia striformis f. sp tritici Eriks (Pst), is a major challenge to resistance breeding in wheat. A genome wide association study (GWAS) was performed using 22,415 single nucleotide polymorphism (SNP) markers and 591 haplotypes to identify genomic regions associated with resistance to YR in a subset panel of 419 pre-breeding lines (PBLs) developed at International Center for Maize and Wheat Improvement (CIMMYT). The 419 PBLs were derived from an initial set of 984 PBLs generated by a three-way crossing scheme (exotic/elite1//elite2) among 25 best elites and 244 exotics (synthetics, landraces) from CIMMYT's germplasm bank. For the study, 419 PBLs were characterized with 22,415 high-quality DArTseq-SNPs and phenotyped for severity of YR disease at five locations in Mexico. A population structure was evident in the panel with three distinct subpopulations, and a genome-wide linkage disequilibrium (LD) decay of 2.5 cM was obtained. Across all five locations, 14 SNPs and 7 haplotype blocks were significantly (P < 0.001) associated with the disease severity explaining 6.0 to 14.1% and 7.9 to 19.9% of variation, respectively. Based on average LD decay of 2.5 cM, identified 14 SNP-trait associations were delimited to seven quantitative trait loci in total. Seven SNPs were part of the two haplotype blocks on chromosome 2A identified in haplotypes-based GWAS. In silico analysis of the identified SNPs showed hits with interesting candidate genes, which are related to pathogenic process or known to regulate induction of genes related to pathogenesis such as those coding for glunolactone oxidase, quinate O-hydroxycinnamoyl transferase, or two-component histidine kinase. The two-component histidine kinase, for example, acts as a sensor in the perception of phytohormones ethylene and cytokinin. Ethylene plays a very important role in regulation of multiple metabolic processes of plants, including induction of defense mechanisms mediated by jasmonate. The SNPs linked to the promising genes identified in the study can be used for marker-assisted selection.

Harnessing genetic potential of wheat germplasm banks through impact-oriented-prebreeding for future food and nutritional security.

The value of exotic wheat genetic resources for accelerating grain yield gains is largely unproven and unrealized. We used next-generation sequencing, together with multi-environment phenotyping, to study the contribution of exotic genomes to 984 three-way-cross-derived (exotic/elite1//elite2) pre-breeding lines (PBLs). Genomic characterization of these lines with haplotype map-based and SNP marker approaches revealed exotic specific imprints of 16.1 to 25.1%, which compares to theoretical expectation of 25%. A rare and favorable haplotype (GT) with 0.4% frequency in gene bank identified on chromosome 6D minimized grain yield (GY) loss under heat stress without GY penalty under irrigated conditions. More specifically, the 'T' allele of the haplotype GT originated in Aegilops tauschii and was absent in all elite lines used in study. In silico analysis of the SNP showed hits with a candidate gene coding for isoflavone reductase IRL-like protein in Ae. tauschii. Rare haplotypes were also identified on chromosomes 1A, 6A and 2B effective against abiotic/biotic stresses. Results demonstrate positive contributions of exotic germplasm to PBLs derived from crosses of exotics with CIMMYT's best elite lines. This is a major impact-oriented pre-breeding effort at CIMMYT, resulting in large-scale development of PBLs for deployment in breeding programs addressing food security under climate change scenarios.

Unlocking the genetic diversity of Creole wheats.

Climate change and slow yield gains pose a major threat to global wheat production. Underutilized genetic resources including landraces and wild relatives are key elements for developing high-yielding and climate-resilient wheat varieties. Landraces introduced into Mexico from Europe, also known as Creole wheats, are adapted to a wide range of climatic regimes and represent a unique genetic resource. Eight thousand four hundred and sixteen wheat landraces representing all dimensions of Mexico were characterized through genotyping-by-sequencing technology. Results revealed sub-groups adapted to specific environments of Mexico. Broadly, accessions from north and south of Mexico showed considerable genetic differentiation. However, a large percentage of landrace accessions were genetically very close, although belonged to different regions most likely due to the recent (nearly five centuries before) introduction of wheat in Mexico. Some of the groups adapted to extreme environments and accumulated high number of rare alleles. Core reference sets were assembled simultaneously using multiple variables, capturing 89% of the rare alleles present in the complete set. Genetic information about Mexican wheat landraces and core reference set can be effectively utilized in next generation wheat varietal improvement.

Exploring and Mobilizing the Gene Bank Biodiversity for Wheat Improvement.

Identifying and mobilizing useful genetic variation from germplasm banks to breeding programs is an important strategy for sustaining crop genetic improvement. The molecular diversity of 1,423 spring bread wheat accessions representing major global production environments was investigated using high quality genotyping-by-sequencing (GBS) loci, and gene-based markers for various adaptive and quality traits. Mean diversity index (DI) estimates revealed synthetic hexaploids to be genetically more diverse (DI= 0.284) than elites (DI = 0.267) and landraces (DI = 0.245). GBS markers discovered thousands of new SNP variations in the landraces which were well known to be adapted to drought (1273 novel GBS SNPs) and heat (4473 novel GBS SNPs) stress environments. This may open new avenues for pre-breeding by enriching the elite germplasm with novel alleles for drought and heat tolerance. Furthermore, new allelic variation for vernalization and glutenin genes was also identified from 47 landraces originating from Iraq, Iran, India, Afghanistan, Pakistan, Uzbekistan and Turkmenistan. The information generated in the study has been utilized to select 200 diverse gene bank accessions to harness their potential in pre-breeding and for allele mining of candidate genes for drought and heat stress tolerance, thus channeling novel variation into breeding pipelines. This research is part of CIMMYT's ongoing 'Seeds of Discovery' project visioning towards the development of high yielding wheat varieties that address future challenges from climate change.

Service patterns of adult survivors of childhood versus adult sexual assault/abuse.

This analysis compared the characteristics and service patterns of adult survivors of childhood sexual assault/abuse and adult survivors of adult sexual assault/abuse. Utilizing data from sexual assault crisis centers serving survivors in a Midwestern state over a six year period and controlling for revictimization, we describe and compare the demographic characteristics, referral sources, and service patterns of the two groups. Results indicate that paths into service differ for the two groups. Furthermore, adult survivors of childhood sexual assault/abuse obtain significantly more hours of service and service contacts on average than adult survivors of adult sexual assault/abuse. Implications for policy and practice are discussed.