bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative transcriptomics of a monocotyledonous geophyte reveals shared molecular mechanisms of underground storage organ formation
Authors: Tribble Carrie M. , Martínez‐Gómez Jesús , Alzate‐Guarín Fernando , Rothfels Carl J. , Specht Chelsea D. 
Published: January 2021

AbstractMany species from across the vascular plant tree‐of‐life have modified standard plant tissues into tubers, bulbs, corms, and other underground storage organs (USOs), unique innovations which allow these plants to retreat underground. Our ability to understand the developmental and evolutionary forces that shape these morphologies is limited by a lack of studies on certain USOs and plant clades. We take a comparative transcriptomics approach to characterizing the molecular mechanisms of tuberous root formation in Bomarea multiflora (Alstroemeriaceae) and compare these mechanisms to those identified in other USOs across diverse plant lineages; B. multiflora fills a key gap in our understanding of USO molecular development as the first monocot with tuberous roots to be the focus of this kind of research. We sequenced transcriptomes from the growing tip of four tissue types (aerial shoot, rhizome, fibrous root, and root tuber) of three individuals of B. multiflora. We identified differentially expressed isoforms between tuberous and non‐tuberous roots and tested the expression of a priori candidate genes implicated in underground storage in other taxa. We identify 271 genes that are differentially expressed in root tubers versus non‐tuberous roots, including genes implicated in cell wall modification, defense response, and starch biosynthesis. We also identify a phosphatidylethanolamine‐binding protein, which has been implicated in tuberization signalling in other taxa and, through gene‐tree analysis, place this copy in a phylogenetic context. These findings suggest that some similar molecular processes underlie the formation of USOs across flowering plants despite the long evolutionary distances among taxa and non‐homologous morphologies (e.g., bulbs vs. tubers). (Plant development, tuberous roots, comparative transcriptomics, geophytes).
Spatially restricted inhibition of cholinergic interneurons in the dorsolateral striatum encourages behavioral exploration
Authors: Amaya Kenneth A. , Smith Kyle S. 
Published: January 2021

AbstractWhen pursuing desirable outcomes, one must make the decision between exploring possible actions to obtain those outcomes and exploiting known strategies to maximize efficiency. The dorsolateral striatum (DLS) has been extensively studied with respect to how actions can develop into habits and has also been implicated as an area involved in governing exploitative behavior. Surprisingly, prior work has shown that DLS cholinergic interneurons (ChIs) are not involved in the canonical habit formation function ascribed to the DLS but are instead modulators of behavioral flexibility after initial learning. To further probe this, we evaluated the role of DLS ChIs in behavioral exploration during a brief instrumental training experiment. Through designer receptors exclusively activated by designer drugs (DREADDs) in ChAT‐Cre rats, ChIs in the DLS were inhibited during specific phases of the experiment: instrumental training, free‐reward delivery, at both times, or never. Without ChI activity during instrumental training, animals biased their responding toward an “optimal” strategy while continuing to work efficiently. This effect was observed again when contingencies were removed as animals with ChIs offline during that phase, regardless of ChI inhibition previously, decreased responding more than animals with ChIs intact. These findings build upon a growing body of literature implicating ChIs in the striatum as gate‐keepers of behavioral flexibility and exploration.
Antibody Prevalence in Epilepsy before Surgery (APES) in drug‐resistant focal epilepsy
Authors: Li Yi , Tymchuk Sarah , Barry John , Muppidi Srikanth , Le Scheherazade 
Published: January 2021

AbstractObjectiveThere is a growing recognition of immune‐mediated causes in patients with focal drug‐resistant epilepsy (DRE); however, they are not systematically assessed in the pre‐surgical diagnostic workup. Early diagnosis and initiation of immunotherapy is associated with a favorable outcome in immune‐mediated seizures. Patients with refractory focal epilepsy with neuronal antibodies (Abs) tend to have a worse surgical prognosis when compared to other etiologies.MethodsWe studied the prevalence of serum Abs in patients ≥18 years of age with DRE of unknown cause before surgery. We proposed and calculated a clinical APES (Antibody Prevalence in Epilepsy before Surgery) score for each subject, which was modified based on Dubey's previously published APE2 score.Results`A total of 335 patients were screened and 86 subjects were included in final analysis. The mean age at the time of recruitment was 44.84 ± 14.86 years, with age at seizure onset 30.89 ± 19.88 years. There were no significant differences among baseline clinical features between retrospective and prospective sub‐cohorts. The prevalence of at least one positive Ab was 33.72%, and central nervous system (CNS)–specific Abs was 8.14%. APES score ≥4 showed slightly better overall prediction (area under the curve [AUC]: 0.84 vs 0.74) and higher sensitivity (100% vs 71.4%), with slightly lower but similar specificity (44.3% vs 49.4%), when compared to APE2 score ≥4. For subjects who had available positron emission tomography (PET) results and all components of APES score (n = 60), the sensitivity of APES score ≥4 yielded a similar prediction potential with an AUC of 0.80.SignificanceOur findings provide persuasive evidence that a subset of patients with focal DRE have potentially immune‐mediated causes. We propose an APES score to help identify patients who may benefit from a workup for immune etiologies during the pre‐surgical evaluation for focal refractory epilepsy with unknown cause.
“I feel like God doesn't like me”: Faith and Ambiguous Loss Among Transgender Youth
Authors: Okrey Anderson Sloan , McGuire Jenifer K. 
Published: January 2021

ObjectiveThe present study expands the use of ambiguous loss theory into the realm of religion and religious rejection for sexual‐ and gender‐minority people, an area that has previously been addressed primarily as an issue of minority stress.BackgroundResearch has demonstrated that religion‐based, nonaffirming messaging from family and faith communities is correlated with decreased health and well‐being of sexual‐ and gender‐minority persons, who are, like most Americans, likely to have been raised in religious (predominately Christian) homes. Existing research has begun to explain why nonaffirming faith affiliation seems to negatively impact sexual gender minority people, but it does not explain the mechanisms of long‐term distress.MethodsThis study is a qualitative thematic analysis of religion and family data from semistructured interviews with 63 transgender youth from the United States, Canada, and Ireland who reported being raised in religious Christian homes.ResultsAnalysis revealed that the narratives of participants who had been members of a psychological family of faith included all of the core elements of ambiguous loss, suggesting that individuals can experience ambiguous loss in relationship to a faith community and to God.DiscussionThis study presents a new application of Boss's ambiguous loss theory and offers a framework for understanding why sexual‐ and gender‐minority people from Christian backgrounds might experience long‐term distress in relation to faith and spirituality whether they stay in their faith communities of origin or move on to something else.ImplicationsThe experiences of transgender people examined through the framework of ambiguous loss and the concept of the psychological family of faith could be applied to research with people from any demographic in relation to loss of faith or faith community. This information may contribute to the study of family ruptures that occur as a result of family experiences of ideological or moral incompatibility (e.g., deconversion, political realignment, leaving a cult).
Precipitation alters the CO2 effect on water‐use efficiency of temperate forests
Authors: Belmecheri Soumaya , Maxwell R. Stockton , Taylor Alan H. , Davis Kenneth J. , Guerrieri Rossella , Moore David J. P. , Rayback Shelly A. 
Published: January 2021

AbstractIncreasing water‐use efficiency (WUE), the ratio of carbon gain to water loss, is a key mechanism that enhances carbon uptake by terrestrial vegetation under rising atmospheric CO2 (ca). Existing theory and empirical evidence suggest a proportional WUE increase in response to rising ca as plants maintain a relatively constant ratio between the leaf intercellular (ci) and ambient (ca) partial CO2 pressure (ci/ca). This has been hypothesized as the main driver of the strengthening of the terrestrial carbon sink over the recent decades. However, proportionality may not characterize CO2 effects on WUE on longer time‐scales and the role of climate in modulating these effects is uncertain. Here, we evaluate long‐term WUE responses to ca and climate from 1901 to 2012 CE by reconstructing intrinsic WUE (iWUE, the ratio of photosynthesis to stomatal conductance) using carbon isotopes in tree rings across temperate forests in the northeastern USA. We show that iWUE increased steadily from 1901 to 1975 CE but remained constant thereafter despite continuously rising ca. This finding is consistent with a passive physiological response to ca and coincides with a shift to significantly wetter conditions across the region. Tree physiology was driven by summer moisture at multi‐decadal time‐scales and did not maintain a constant ci/ca in response to rising ca indicating that a point was reached where rising CO2 had a diminishing effect on tree iWUE. Our results challenge the mechanism, magnitude, and persistence of CO2's effect on iWUE with significant implications for projections of terrestrial productivity under a changing climate.
Major and persistent shifts in below‐ground carbon dynamics and soil respiration following logging in tropical forests
Authors: Riutta Terhi , Kho Lip Khoon , Teh Yit Arn , Ewers Robert , Majalap Noreen , Malhi Yadvinder 
Published: January 2021

AbstractSoil respiration is the largest carbon efflux from the terrestrial ecosystem to the atmosphere, and selective logging influences soil respiration via changes in abiotic (temperature, moisture) and biotic (biomass, productivity, quantity and quality of necromass inputs) drivers. Logged forests are a predominant feature of the tropical forest landscape, their area exceeding that of intact forest. We quantified both total and component (root, mycorrhiza, litter, and soil organic matter, SOM) soil respiration in logged (n = 5) and old‐growth (n = 6) forest plots in Malaysian Borneo, a region which is a global hotspot for emission from forest degradation. We constructed a detailed below‐ground carbon budget including organic carbon inputs into the system via litterfall and root turnover. Total soil respiration was significantly higher in logged forests than in old‐growth forests (14.3 ± 0.23 and 12.7 ± 0.60 Mg C ha−1 year−1, respectively, p = 0.037). This was mainly due to the higher SOM respiration in logged forests (55 ± 3.1% of the total respiration in logged forests vs. 50 ± 3.0% in old‐growth forests). In old‐growth forests, annual SOM respiration was equal to the organic carbon inputs into the soil (difference between SOM respiration and inputs 0.18 Mg C ha−1 year−1, with 90% confidence intervals of −0.41 and 0.74 Mg C ha−1 year−1), indicating that the system is in equilibrium, while in logged forests SOM respiration exceeded the inputs by 4.2 Mg C ha−1 year−1 (90% CI of 3.6 and 4.9 Mg C ha−1 year−1), indicating that the soil is losing carbon. These results contribute towards understanding the impact of logging on below‐ground carbon dynamics, which is one of the key uncertainties in estimating emissions from forest degradation. This study demonstrates how significant perturbation of the below‐ground carbon balance, and consequent net soil carbon emissions, can persist for decades after a logging event in tropical forests.
Olfactory‐cognitive index distinguishes involvement of frontal lobe shrinkage, as in sarcopenia from shrinkage of medial temporal areas, and global brain, as in Kihon Checklist frailty/dependence, in older adults with progression of normal cognition to Alzheimer's disease
Authors: Iritani Osamu , Okuno Tazuo , Miwa Takaki , Makizako Hyuma , Okutani Fumino , Kashibayashi Tetsuo , Suzuki Kumiko , Hara Hideo , Mori Eri , Omoto Shusaku , Suzuki Hirokazu , Shibata Minori , Adachi Hiroaki , Kondo Kenji , Umeda‐Kameyama Yumi , Kodera Kumie , Morimoto Shigeto 
Published: January 2021

AimOlfactory impairment as a prodromal symptom, as well as sarcopenia, frailty and dependence as geriatric syndromes, is often associated with cognitive decline in older adults with progression of Alzheimer's disease. The present study aimed to evaluate the associations of olfactory and cognitive decline with these geriatric syndromes, and with structural changes of the brain in older adults.MethodsThe participants were 135 older adults (47 men and 88 women, mean age 79.5 years), consisting of 64 with normal cognition, 23 with mild cognitive impairment and 48 with Alzheimer's disease. Olfactory function was evaluated by the Open Essence odor identification test. Shrinkage of the regional brain was determined by magnetic resonance imaging.ResultsLogistic regression analysis with Open Essence, Mini‐Mental State Examination, age and sex as covariates showed higher olfactory‐cognitive index (|coefficient for Open Essence (a) / coefficient for Mini‐Mental State Examination (b)|) in participants with sarcopenia (Asia Working Group for Sarcopenia), and lower values of (|a/b|) in participants with Barthel Index dependence, Kihon Checklist frailty, Lawton Index dependence and support/care‐need certification as objective variables. Logistic regression analysis adjusted by age and sex also showed significant shrinkage of the frontal lobe in participants with AWGS sarcopenia, especially in women, and shrinkage of the medial temporal areas and global brain in participants with Kihon Checklist frailty/dependence.ConclusionsOlfactory‐cognitive index (|a/b|) might be a useful tool to distinguish involvement of frontal lobe shrinkage, as in sarcopenia from shrinkage of the medial temporal areas, and global brain, as in frailty/dependence, in older adults with progression of normal cognition to Alzheimer's disease. Geriatr Gerontol Int 2021; ••: ••–••.
A New Randomized Binary Prior Model for Hydraulic Tomography in Fractured Aquifers
Authors: Poduri Sarada , Kambhammettu BVNP , Gorugantula Saisrinivas 
Published: January 2021

AbstractWe present a novel pilot‐point‐based hydraulic tomography (HT) inversion procedure to delineate preferential flow paths and estimate hydraulic properties in a fractured aquifer. Our procedure considers a binary prior model developed using a randomized algorithm. The randomized algorithm involves discretizing the domain into grid cells, assigning a binary label to each cell, traversing the grid randomly, and choosing the optimal grid configuration cell‐by‐cell. This binary prior model is used to guide the placement of pilot points and to constrain aquifer parameters during pilot‐point‐based HT inversion. A two‐dimensional fractured granite rock block was considered to test our methodology under controlled laboratory conditions. Multiple pumping tests were conducted at selected ports and the pressure responses were monitored. The pumping datasets thus obtained were preprocessed using median filters to remove random noise, and then analyzed using the proposed procedure. The proposed binary prior algorithm was implemented in C++ by supplying the forward groundwater model, HydroGeoSphere (HGS). Pilot‐point‐assisted HT inversion was performed using the parameter‐estimation tool, coupled to HGS. The resulting parameter distributions were assessed by: (1) a visual comparison of the K‐ and Ss‐tomograms with the known topology of the fractures and (2) comparing model predictions with measurements made at two validation ports that were not used in calibration. The performance assessment revealed that HT with the proposed randomized binary prior could be used to recover fracture‐connectivity and to predict drawdowns in fractured aquifers with reasonable accuracy, when compared to a conventional pilot‐point inversion scheme.
Fiber Optic Measurements of Soil Moisture in a Waste Rock Pile
Authors: Wu Robert , Martin Vincent , McKenzie Jeffrey M. , Broda Stefan , Bussière Bruno , Selker John , Aubertin Michel 
Published: January 2021

AbstractThe design and construction of a waste rock pile influences water infiltration and may promote the production of contaminated mine drainage. The objective of this project is to evaluate the use of an active fiber optic distributed temperature sensing (aFO‐DTS) protocol to measure infiltration and soil moisture within a flow control layer capping an experimental waste rock pile. Five hundred meters of fiber optic cable were installed in a waste rock pile that is 70 m long, 10 m wide, and was covered with 0.60 m of fine compacted sand and 0.25 m of non‐reactive crushed waste rock. Volumetric water content was assessed by heating the fiber optic cable with 15‐min heat pulses at 15 W/m every 30 min. To test the aFO‐DTS system 14 mm of recharge was applied to the top surface of the waste rock pile over 4 h, simulating a major rain event. The average volumetric water content in the FCL increased from 0.10 to 0.24 over the duration of the test. The volumetric water content measured with aFO‐DTS in the FCL and waste rock was within ±0.06 and ±0.03, respectively, compared with values measured using 96 dielectric soil moisture probes over the same time period. Additional results illustrate how water can be confined within the FCL and monitored through an aFO‐DTS protocol serving as a practical means to measure soil moisture at an industrial capacity.
Migration of Injected Wastewater with High Levels of Ammonia in a Saline Aquifer in South Florida
Authors: Sepúlveda Nicasio , Lohmann Melinda 
Published: January 2021

AbstractTreated wastewater with high levels of ammonia has been injected, since March 1983 into the deep saline units of the Lower Floridan aquifer (LFA) from a treatment plant near the east coast of Miami‐Dade County in southeastern Florida. Monitoring wells in the plant recorded ammonia concentrations above ambient levels at hydrogeologic units located about 1000 ft (304.8 m) above injection depths between 2500 and 2800 ft (762 and 853 m) below sea level. A solute‐transport model was developed to assess the horizontal and vertical extent of the injected ammonia, with ammonia moving from the injected zone into the overlying units: the upper semiconfining unit, the uppermost permeable zone of the LFA, and the middle semiconfining units of the Avon Park Formation. Ammonia is assumed to be transported under the effects of local heterogeneity in a porous limestone aquifer with high‐salinity ambient groundwater and via upward migration through quasi‐vertical pathways. A flow model of the migration of the injected ammonia was calibrated with PEST using head, salinity, and ammonia concentration data measured from 1983 to 2013. Borehole geophysical data support the high permeability of the uppermost permeable zone in the LFA. Average simulated head, normalized salinity, and ammonia concentration residuals over all monitoring wells were −1.37 ft, 0.01, and −0.67 mg/L, respectively. Model results are consistent with undetectable ammonia concentrations in the Upper Floridan aquifer.
Barriers and challenges of returning patients back to community after renal transplantation in Central Australia
Authors: Karepalli Vijay K. , Brown Megan , Sajiv Cherian , Fernandes David , Thomas Sajan , George Pratish , Nayar Sajith , Pawar Basant 
Published: January 2021

AbstractBackgroundThe majority of patients living in remote communities of Central Australia must relocate to Alice Springs for their dialysis treatments. There is limited information available about the challenges and barriers that Aboriginal patients encounter in the process of returning back to their communities after renal transplantation.AimTo determine the length of stay of patients in Alice Springs and challenges faced subsequent to renal transplantation, before they could safely return to their remote communities.MethodsAll transplant recipients from 2012 who are aged 18 years were analysed retrospectively.ResultsThirty‐six patients received renal transplantation from Central Australia. Of them, 25 were from very remote communities of whom 24 were Aboriginal. Average length of stay in Alice Springs post‐transplantation prior to returning to community was 17.2 weeks (121 days). The most common challenge faced prior to returning to community was the need for monitoring and titration of immunosuppressive medication (100%) followed by infections (90%) and admissions to hospital (85%). The other common barrier was optimising glycaemic control (80%). Less common barriers included proficiency with self‐monitoring of blood sugar levels (50%), social factors (40%), blood pressure control (25%), leukopenia (25%), safe housing (20%) and rejection episodes (15%).ConclusionsMultiple challenges are faced during post‐transplantation period in Alice Springs that prolong the time before recipients from remote communities can return home. Some barriers such as titration of immunosuppression are inherent in the transplant journey. However, some factors might be modifiable prior to transplantation.
Demystifying machine learning: a primer for physicians
Authors: Scott Ian A. 
Published: January 2021

AbstractMachine learning is a tool for analysing digitised data sets and formulating predictions that can optimise clinical decision‐making. It aims to identify complex patterns in large data sets and encode them into models that can then classify new unseen cases or make predictions on new data. Machine learning methods take several forms and individual models can be of many different types. More than 50 models have been approved for use in routine healthcare, and the numbers continue to grow exponentially. The reliability and robustness of any model depends on multiple factors, including the quality and quantity of the data used to develop the models, and the selection of features in the data considered most important to maximising accuracy. In ensuring models are safe, effective and reproducible in routine care, physicians need to have some understanding of how these models are developed and evaluated, and to collaborate with data and computer scientists in their design and validation. This narrative review introduces principles, methods and examples of machine learning in a way that does not require mastery of highly complex statistical and computational concepts.