Using GIS-based and remotely sensed data for early winter moose (Alces alces gigas) survey stratification

Thesis (M.S.) University of Alaska Fairbanks, 2005Stratification of moose survey areas is a key step to reduce population estimation variance. In the Yukon and Alaska, use of fixed-area grids for early winter moose counts combined with the increasing availability of GIS and remotely sensed data provide the opportunity to develop standardized and repeatable habitat-based stratifications. I used univariate comparisons, stepwise regression and AIC modeling to describe moose distribution as a function of landscape level variables for an area in west central Yukon during 1998 and 1999. Results quantified early winter habitat use of upland shrub habitats and support previous observations for early winter moose habitat use in Alaska, Minnesota and Montana. Number of patches, in association with areas of alpine and shrubs, were found to be highly influential for survey blocks where moose are expected to be present and in high numbers. Overall, model performance based on relative abundance of moose was less predictive than for blocks where moose were present or absent. Spatial resolution of GIS and remotely sensed data used in this study (25 m grid cells) provided sufficient spatial detail to generate correlations between moose presence and habitat for a first level stratification.Introduction -- Study area -- Early winter moose surveys -- Land cover mapping -- Habitat variables -- Statistical analyses -- Model development and assessment -- Results -- Early winter moose Surveys --Land cover mapping -- Moose presence and absence -- Univariate analyses -- Stepwise regression -- Model assessment -- High/low numbers of observed adult moose -- Univariate analysis -- Stepwise regression -- Model assessment -- Discussion -- Limitations of this study -- Conclusions and recommendation -- Recommendations for conducting habitat-based stratifications -- Literature cited -- List of personal communication -- Tables -- Figures -- Appendices

Apparent Predation of an American Water Shrew, Sorex palustris, by an American Marten, Martes americana

Little is known of the natural history of American Water Shrews, Sorex palustris, including their predators. We document an apparent case of predation of an American Water Shrew by an American Marten, Martes americana, in the boreal forest of southeastern Yukon

Pressure Injuries in Nursing Homes: Investigating Racial/Ethnic Differences Using National Data

Context: In the United States, Black nursing home (NH) residents have higher rates of pressure injury (PI) than White residents. Although some studies ascribe this to a relatively high proportion of Black residents in NHs with poor outcomes and limited resources, the factors that associate with PIs and their consequences across and within NHs remain poorly understood. Also, little is known about PIs among residents of differing races and ethnicities. Objectives: Using four national datasets from 2016–2017, we evaluated U.S. NHs to characterize differences in PI-related outcomes among non-Hispanic Whites, non-Hispanic Blacks, Hispanics, Asians, American Indian or Alaska Natives, and Native Hawaiian or Other Pacific Islanders, and clarified the impact of resident-, facility-, and community-level characteristics on these outcomes. Methods: We calculated the annual incidence rate of PIs, the probability of PI healing, and the prevalence of PI-associated pain and analgesic prescription. We determined the bivariate associations between each of these outcomes and race/ethnicity, and between each outcome and multiple potential covariates. Multivariable analyses then evaluated the associations between each outcome and race/ethnicity while adjusting for covariates. Findings: In the bivariate analyses, the annual incidence rate of stage 2, 3, 4, and unstageable PIs for Whites was lower than Blacks and Hispanics, similar to American Indians or Alaska Natives, and higher than Asians and Native Hawaiians or Other Pacific Islanders. In the multivariable analyses, the PI incidence rate ratio was higher only among American Indians or Alaska Natives, and this difference was associated with a NH-level variable—the proportion of racial and ethnic minority residents. Other outcomes did not vary by race/ethnicity. An adjusted exploratory analysis was conducted to help explain the difference between the bivariate and multivariable analyses and revealed an important within-NH difference: Compared to Whites, the PI incidence rate ratios were higher in women who were Black, or American Indian or Alaska Native. Limitations: Our findings are correlational and may be impacted by unevaluated variables and the limitations of administrative data. Implications: In U.S. NHs, the annual incidence rate of PIs varies by race/ethnicity. Facility characteristics strongly influence this variation. Higher incidence rate ratios among racial and ethnic minority residents also are explained by differences within NHs and are striking among subgroups, including female residents who are Black, or American Indian or Alaska Native. Future research should evaluate the sexes separately and explore both across-NH and within-NH differences to determine whether there are structural inequities, bias, and disparate care

Designer diatom episomes delivered by bacterial conjugation.

Eukaryotic microalgae hold great promise for the bioproduction of fuels and higher value chemicals. However, compared with model genetic organisms such as Escherichia coli and Saccharomyces cerevisiae, characterization of the complex biology and biochemistry of algae and strain improvement has been hampered by the inefficient genetic tools. To date, many algal species are transformable only via particle bombardment, and the introduced DNA is integrated randomly into the nuclear genome. Here we describe the first nuclear episomal vector for diatoms and a plasmid delivery method via conjugation from Escherichia coli to the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana. We identify a yeast-derived sequence that enables stable episome replication in these diatoms even in the absence of antibiotic selection and show that episomes are maintained as closed circles at copy number equivalent to native chromosomes. This highly efficient genetic system facilitates high-throughput functional characterization of algal genes and accelerates molecular phytoplankton research

Yield of colorectal cancer at colonoscopy according to faecal haemoglobin concentration in symptomatic patients referred from primary care

Background: Lower gastrointestinal (GI) symptoms are poor predictors of colorectal cancer (CRC). This study examined the diagnostic yield of colonoscopy by faecal haemoglobin concentration (f‐Hb) in symptomatic patients assessed in primary care by faecal immunochemical testing (FIT). Methods: In three Scottish NHS Boards, FIT kits (HM‐JACKarc, Hitachi Chemical Diagnostics Systems Co., Ltd, Tokyo, Japan) were used by GPs to guide referrals for patients with lower GI symptoms (lab data studied for 12 months from December 2015 onward in Tayside, 18 months from June 2018 onward in Fife, and 5 months from September 2018 onward in Greater Glasgow and Clyde). CRC cases diagnosed at colonoscopy were ascertained from colonoscopy and pathology records. Results: 4841 symptomatic patients who underwent colonoscopy after FIT submission were included. Of 2166 patients (44.7%) with f‐Hb <10 µg Hb/g faeces (µg/g), 14 (0.6%) were diagnosed with CRC, with a number needed to scope (NNS) of 155. Of 2675 patients (55.3%) with f‐Hb ≥10 µg/g, 252 were diagnosed with CRC (9.4%) with a NNS of 11. Of 705 patients with f‐Hb ≥400 µg/g, 158 (22.4%) were diagnosed with CRC with a NNS of 5. Over half of those diagnosed with CRC with f‐Hb <10 µg/g had co‐existing anaemia. Conclusions: Symptomatic patients with f‐Hb ≥10 µg/g should undergo further investigation for CRC, while higher f‐Hb could be used to triage its urgency during the COVID‐19 recovery phase. Patients with f‐Hb <10 µg/g, without anaemia, are very unlikely to be diagnosed with CRC and the majority need no further investigation

Risk of Cancer Death Among White, Black, and Hispanic Populations in South Florida

Background: The cancer burden in South Florida, with a population of more than 6 million with a heavily Hispanic and large Afro-Caribbean population, has not been quantified. Methods: We analyzed 2012–2016 cancer mortality data from South Florida for white, Hispanic, and black populations with disaggregation for Cuban, Puerto Rican, South American, African American, and Afro-Caribbean groups. We calculated cancer site-specific and all-sites combined age-adjusted mortality rates, and we used negative binomial regression to determine mortality rate ratios to compare South Florida’s cancer mortality rates with those of the rest of the nation. Results: We analyzed 53,837 cancer deaths. Per 100,000 population, cancer mortality rates in South Florida were similar among white (173 per 100,000) and black (176 per 100,000) men and among white and black women (133 for both), and they were lowest among Hispanic men (151 per 100,000) and women (93 per 100,000). However, compared with their counterparts nationally, Hispanic residents in South Florida had higher cancer mortality rates, largely driven by Cuban residents, and mortality rates among white and black residents, especially male residents, were substantially lower. Liver cancer rates were high among white and Puerto Rican “baby boomers”; lung cancer mortality was low among all groups except Cuban men; cervical cancer was high among white, black, and Puerto Rican women. Conclusion: Cancer patterns are not monochromatic in all US regions; South Florida is distinctive. Meeting the needs of an aging diverse population presents challenges for all major metropolitan areas. Expanding surveillance, increasing minority participation in clinical trials, and investing in culturally specific community-based health promotion must continue

Simple Guide to Using Generative Artificial Intelligence Writing Tools in Research & Scholarship at UNH

While Artificial Intelligence (AI) technologies have existed for years, the recent arrival of widespread generative AI writing tools such as ChatGPT has provoked varied reactions in the scholarly community worldwide. Undoubtedly easy access to such tools may help to level the scholarly playing field for certain groups, particularly those with limited writing skills or proficiency with English as the primary language for written and oral communication of research and scholarship. There are, however, concerns about these tools, including, but not limited to, the accuracy, consistency, and bias of the information generated, appropriate acknowledgement of source material, and the tools’ lack of ability to reason or to understand meaning when generating output. This simple guide was developed to assist researchers and trainees to understand the fundamental issues with these technologies regarding research integrity

Deep Sequencing Reveals Direct Targets of Gammaherpesvirus-Induced mRNA Decay and Suggests That Multiple Mechanisms Govern Cellular Transcript Escape

One characteristic of lytic infection with gammaherpesviruses, including Kaposi's sarcoma-associated herpesvirus (KSHV), Epstein-Barr virus (EBV) and murine herpesvirus 68 (MHV68), is the dramatic suppression of cellular gene expression in a process known as host shutoff. The alkaline exonuclease proteins (KSHV SOX, MHV-68 muSOX and EBV BGLF5) have been shown to induce shutoff by destabilizing cellular mRNAs. Here we extend previous analyses of cellular mRNA abundance during lytic infection to characterize the effects of SOX and muSOX, in the absence of other viral genes, utilizing deep sequencing technology (RNA-seq). Consistent with previous observations during lytic infection, the majority of transcripts are downregulated in cells expressing either SOX or muSOX, with muSOX acting as a more potent shutoff factor than SOX. Moreover, most cellular messages fall into the same expression class in both SOX- and muSOX-expressing cells, indicating that both factors target similar pools of mRNAs. More abundant mRNAs are more efficiently downregulated, suggesting a concentration effect in transcript targeting. However, even among highly expressed genes there are mRNAs that escape host shutoff. Further characterization of select escapees reveals multiple mechanisms by which cellular genes can evade downregulation. While some mRNAs are directly refractory to SOX, the steady state levels of others remain unchanged, presumably as a consequence of downstream effects on mRNA biogenesis. Collectively, these studies lay the framework for dissecting the mechanisms underlying the susceptibility of mRNA to destruction during lytic gammaherpesvirus infection

ENIGMA and global neuroscience: A decade of large-scale studies of the brain in health and disease across more than 40 countries.

This review summarizes the last decade of work by the ENIGMA (Enhancing NeuroImaging Genetics through Meta Analysis) Consortium, a global alliance of over 1400 scientists across 43 countries, studying the human brain in health and disease. Building on large-scale genetic studies that discovered the first robustly replicated genetic loci associated with brain metrics, ENIGMA has diversified into over 50 working groups (WGs), pooling worldwide data and expertise to answer fundamental questions in neuroscience, psychiatry, neurology, and genetics. Most ENIGMA WGs focus on specific psychiatric and neurological conditions, other WGs study normal variation due to sex and gender differences, or development and aging; still other WGs develop methodological pipelines and tools to facilitate harmonized analyses of "big data" (i.e., genetic and epigenetic data, multimodal MRI, and electroencephalography data). These international efforts have yielded the largest neuroimaging studies to date in schizophrenia, bipolar disorder, major depressive disorder, post-traumatic stress disorder, substance use disorders, obsessive-compulsive disorder, attention-deficit/hyperactivity disorder, autism spectrum disorders, epilepsy, and 22q11.2 deletion syndrome. More recent ENIGMA WGs have formed to study anxiety disorders, suicidal thoughts and behavior, sleep and insomnia, eating disorders, irritability, brain injury, antisocial personality and conduct disorder, and dissociative identity disorder. Here, we summarize the first decade of ENIGMA's activities and ongoing projects, and describe the successes and challenges encountered along the way. We highlight the advantages of collaborative large-scale coordinated data analyses for testing reproducibility and robustness of findings, offering the opportunity to identify brain systems involved in clinical syndromes across diverse samples and associated genetic, environmental, demographic, cognitive, and psychosocial factors