bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmental variables and genome-environment interactions predicting IBD diagnosis in large UK cohort
Authors: Yang Alan Z. , Jostins-Dean Luke 
Published: June 2022

AbstractA combination of genetic susceptibility and environmental exposure is thought to cause inflammatory bowel disease (IBD), but the non-genetic component remains poorly characterized. We therefore undertook a search for environmental variables and gene-environment interactions associated with future IBD diagnosis in a large UK cohort. Using self-report and electronic health records, we identified 1946 Crohn’s disease (CD) and 3715 ulcerative colitis (UC) patients after quality control in the UK Biobank. Based on prior literature and biological plausibility
, we tested 38 candidate environmental variables for association with CD, UC, and overall IBD using Cox proportional hazard regressions. We also tested whether these variables interacted with polygenic risk in predicting disease, following up significant (FDR < 0.05) results with tests for SNP-environment associations. We performed robustness analyses on all significant results. As in previous reports, appendectomy protected against UC, smoking (both current and previous) elevated risk for CD, current smoking protected against UC, and previous smoking imparted a risk for UC. Childhood antibiotic use associated with IBD, as did sun exposure during the winter. Socioeconomic deprivation was conferred a risk for IBD, CD, and UC. We uncovered negative interactions between polygenic risk and previous oral contraceptive use for IBD and UC. Polygenic risk also interacted negatively with previous smoking in predicting UC. There were no individually significant SNP-environment interactions. Thus, for a limited set of environmental variables, there was strong evidence of association with IBD diagnosis in the UK Biobank, and interaction with polygenic risk was minimal.
Anatomy-dependent lung doses from 3D-conformal breast-cancer radiotherapy
Authors: Kundrát Pavel , Rennau Hannes , Remmele Julia , Sebb Sabine , Simonetto Cristoforo , Kaiser Jan Christian , Hildebrandt Guido , Wolf Ulrich , Eidemüller Markus 
Published: June 2022

AbstractThis study aims to identify key anatomic features that govern the individual variability of lung doses from breast-cancer radiotherapy. 3D conformal, intensity-modulated and hybrid techniques with 50.4 Gy whole-breast dose were planned for 128 patients. From their CT images, 17 anatomic measures were assessed and tested as predictors for lung dose-volume characteristics. Tangential techniques yielded mean ipsilateral lung doses in the range of 3–11 Gy. This inter-patient variability was explained to almost 40% by central lung distance, and to almost 60% if this measure was complemented by midplane lung width and maximum heart distance. Also the variability in further dose-volume metrics such as volume fractions receiving 5, 20 or 40 Gy could be largely explained by the anatomy. Multi-field intensity-modulated radiotherapy reduced high-exposed lung volumes, but resulted in higher mean ipsilateral lung doses and larger low-dose burden. Contralateral lung doses ranged from 0.3 to 1 Gy. The results highlight that there are large differences in lung doses among breast-cancer patients. Most of this inter-individual variability can be explained by a few anatomic features. The results will be implemented in a dedicated software tool to provide personalized estimates of long-term health risks related to breast-cancer radiotherapy. The results may also be used to identify favourable as well as problematic anatomies, and serve as a quick quantitative benchmark for individual treatment plans.
Determination of lipid requirements in black soldier fly through semi-purified diets
Authors: Bellezza Oddon S. , Biasato I. , Resconi A. , Gasco L. 
Published: June 2022

AbstractThe insect market is still far from an effective upscale and, to achieve this goal, it is necessary to know the BSF dietary requirements for the production maximization. Worldwide, given the waste variability, is not always easy to identify the optimal waste-based mixture that can allow to reach the best production, in terms of quantity and quality. Due this reason, nutritional need ranges are the basic knowledge, affordable for everyone, to increase the profitability of the insect farming. The study aims to evaluate the effects of 6 semi-purified, isonitrogenous and isoenergetic diets (SPII) with increasing lipid levels (1%, L1; 1.5%, L1.5; 2.5%, L2.5; 3.5% L3.5; 4.5%, L4.5) on BSF life history traits (6 replicates/treatment and 100 larvae/replicate). The Gainesville diet was used as environmental control. Considering the whole larval stage, 4.5% lipid level guarantees better performance when compared to content lower than 2.5%. The L4.5 10-day-old larvae yielded greater when compared to the other dietary treatments. At 14 and 18 days of age, the larvae of the groups above 2.5% performed better than L1, while the L1.5 showed intermediate results. Lipid levels below 1.5% on DM, when compared to 4.5%, resulted in a smaller prepupa and pupa size. The results obtained on the adult stage do not allow the identification of a lipid levels ideal range, as in the larval stage. In conclusion, in the whole larval stage and in prepupae/pupae phases, lipid percentage lower than (or equal to) 1% have a negative effect on growth. Other research will be needed in order to evaluate lipid levels above 4.5% on DM.
Effects of animal-assisted psychotherapy incorporating mindfulness and self-compassion in neurorehabilitation: a randomized controlled feasibility trial
Authors: Künzi Pascale , Ackert Michael , grosse Holtforth Martin , Hund-Georgiadis Margret , Hediger Karin 
Published: June 2022

AbstractTransdiagnostic psychotherapeutic approaches are increasingly used in neurorehabilitation to address psychological distress. Animal-assistance is thought to increase efficacy. The present study evaluates a psychotherapeutic mindfulness- and self-compassion-based group intervention (MSCBI) with and without animal-assistance for patients with acquired brain injury. Patients (N = 31) were randomly assigned to the 6-week intervention with (n = 14) or without animal-assistance (n = 17). Primary outcome was psychological distress at post- and follow-up treatment, secondary outcomes were changes within-session of patients’ emotional states, adherence to treatment and attrition. Psychological distress significantly decreased in both groups from pre- to follow-up treatment with no difference between groups. Patients in the animal-assisted MSCBI group reported significantly higher increases in feeling secure, accepted, comforted, grateful, motivated and at ease during the sessions compared to patients in the MSCBI group without animal-assistance. Adherence to sessions was significantly higher in the animal-assisted MSCBI group. Attrition did not significantly differ between groups. Our results show that both MSCBIs with and without animal-assistance are feasible and effective in reducing psychological distress in patients with acquired brain injury. The significant changes within-sessions mainly in relationship-based emotional states and the higher treatment adherence suggest additional effects of animal-assistance. Animal-assistance might increase acceptability and patients’ commitment to psychotherapy.
Fully inkjet-printed flexible organic voltage inverters as a basic component in digital NOT gates
Authors: Luczak Adam , Mitra Kalyan Y. , Baumann Reinhard R. , Zichner Ralf , Luszczynska Beata , Jung Jaroslaw 
Published: June 2022

AbstractIn relation to conventional vacuum-based processing techniques inkjet printing enables upscaling fabrication of basic electronic elements, such as transistors and diodes. We present the fully inkjet printed flexible electronic circuits, including organic voltage inverter which can work as a NOT logic gate. For this purpose the special ink compositions were formulated to preparation of gate dielectric layer containing poly (4-vinylphenol) and of the semiconductor layer poly[2,5-(2-octyldodecyl)-3,6-diketopyrrolopyrrole-alt-5,5-(2,5-di(thien-2-yl)thieno [3,2-b]thiophene)]. A printed photoxidized poly (3-hexyltiophene) semiconductor was used as the active layer of the resistors. The operation of the printed inverters and NOT logic gates was analyzed based on the DC current–voltage characteristics of the devices. The resistance of the devices to atmospheric air was also tested. Not encapsulated samples stored for three years under ambient conditions. Followed by annealing to remove moisture showed unchanged electrical parameters in comparison to freshly printed samples.
Renal transcriptome profiles in mice reveal the need for sufficient water intake irrespective of the drinking water type
Authors: Shon Woo-Jeong , Park Mi-Na , Lee Jooyoung , Shin Ji-Hee , Shin Dong-Mi 
Published: June 2022

AbstractThis study sought to characterize the impact of long-term dehydration in terms of physiological and biochemical parameters, as well as renal transcriptomes. Furthermore, we assessed whether consumption of specific types of water elicit more beneficial effects on these health parameters. To this end, C57BL/6 mice were either provided water for 15 min/day over 2 and 4 weeks (water restricted; RES), or ad libitum access to distilled (CON), tap, spring, or purified water. Results show that water restriction decreases urine output and hematocrit levels while increasing brain vasopressin mRNA levels in RES mice compared to control mice (CON). Meanwhile, blood urea nitrogen and creatinine levels were higher in the RES group compared to the CON group. Kidney transcriptome analysis further identified kidney damage as the most significant biological process modulated by dehydration. Mechanistically, prolonged dehydration induces kidney damage by suppressing the NRF2-signaling pathway, which targets the cytoprotective defense system. However, type of drinking water does not appear to impact physiological or blood biochemical parameters, nor the renal transcriptome profile, suggesting that sufficient water consumption is critical, irrespective of the water type. Importantly, these findings also inform practical action for environmental sustainability by providing a theoretical basis for reducing bottled water consumption.
A model-specific simplification of the Mouse Grimace Scale based on the pain response of intraperitoneal CCl4 injections
Authors: Ernst Lisa , Bruch Stefan , Kopaczka Marcin , Merhof Dorit , Bleich André , Tolba René H. , Talbot Steven R. 
Published: June 2022

AbstractDespite its long establishment and applicability in mice pain detection, the Mouse Grimace Scale still seems to be underused in acute pain detection during chronic experiments. However, broadening its applicability can identify possible refinement approaches such as cumulative severity and habituation to painful stimuli. Therefore, this study focuses on two main aspects: First, five composite MGS criteria were evaluated with two independent methods (the MoBPs algorithm and a penalized least squares regression) and ranked for their relative importance. The most important variable was used in a second analysis to specifically evaluate the context of pain after an i.p. injection (intervention) in two treatment groups (CCl4 and oil (control)) at fixed times throughout four weeks in 24 male C57BL/6 N mice. One hour before and after each intervention, video recordings were taken, and the MGS assessment was performed. In this study, the results indicate orbital tightening as the most important criterion. In this experimental setup, a highly significant difference after treatment between week 0 and 1 was found in the CCl4 group, resulting in a medium-sized effect (W = 62.5, p value < 0.0001, rCCl4 = 0.64). The oil group showed no significant difference (week 0 vs 1, W = 291.5, p value = 0.7875, rcontrol = 0.04). Therefore, the study showed that the pain caused by i.p. injections was only dependent on the applied substance, and no significant cumulation or habituation occurred due to the intervention. Further, the results indicated that the MGS system can be simplified.
Comparison of anxiety-like and social behaviour in medaka and zebrafish
Authors: Lucon-Xiccato Tyrone , Loosli Felix , Conti Francesca , Foulkes Nicholas S. , Bertolucci Cristiano 
Published: June 2022

AbstractThe medaka, Oryzias latipes, is rapidly growing in importance as a model in behavioural research. However, our knowledge of its behaviour is still incomplete. In this study, we analysed the performance of medaka in 3 tests for anxiety-like behaviour (open-field test, scototaxis test, and diving test) and in 3 sociability tests (shoaling test with live stimuli, octagonal mirror test, and a modified shoaling test with mirror stimulus). The behavioural response of medaka was qualitatively similar to that observed in other teleosts in the open-field test (thigmotaxis), and in 2 sociability tests, the shoaling test and in the octagonal mirror test (attraction towards the social stimulus). In the remaining tests, medaka did not show typical anxiety (i.e., avoidance of light environments and preference for swimming at the bottom of the aquarium) and social responses (attraction towards the social stimulus). As a reference, we compared the behaviour of the medaka to that of a teleost species with well-studied behaviour, the zebrafish, tested under the same conditions. This interspecies comparison indicates several quantitative and qualitative differences across all tests, providing further evidence that the medaka responds differently to the experimental settings compared to other fish models.
Immediate impact of yogic breathing on pulsatile cerebrospinal fluid dynamics
Authors: Yildiz Selda , Grinstead John , Hildebrand Andrea , Oshinski John , Rooney William D. , Lim Miranda M. , Oken Barry 
Published: June 2022

AbstractCerebrospinal fluid (CSF), a clear fluid bathing the central nervous system (CNS), undergoes pulsatile movements. Together with interstitial fluid, CSF plays a critical role for the removal of waste products from the brain, and maintenance of the CNS health. As such, understanding the mechanisms driving CSF movement is of high scientific and clinical impact. Since pulsatile CSF dynamics is sensitive and synchronous to respiratory movements, we are interested in identifying potential integrative therapies such as yogic breathing to regulate CSF dynamics, which has not been reported before. Here, we investigated the pre-intervention baseline data from our ongoing randomized controlled trial, and examined the impact of four yogic breathing patterns: (i) slow, (ii) deep abdominal, (iii) deep diaphragmatic, and (iv) deep chest breathing with the last three together forming a yogic breathing called three-part breath. We utilized our previously established non-invasive real-time phase contrast magnetic resonance imaging approach using a 3T MRI instrument, computed and tested differences in single voxel CSF velocities (instantaneous, respiratory, cardiac 1st and 2nd harmonics) at the level of foramen magnum during spontaneous versus yogic breathing. In examinations of 18 healthy participants (eight females, ten males; mean age 34.9 ± 14 (SD) years; age range: 18–61 years), we observed immediate increase in cranially-directed velocities of instantaneous-CSF 16–28% and respiratory-CSF 60–118% during four breathing patterns compared to spontaneous breathing, with the greatest changes during deep abdominal breathing (28%, p = 0.0008, and 118%, p = 0.0001, respectively). Cardiac pulsation was the primary source of pulsatile CSF motion except during deep abdominal breathing, when there was a comparable contribution of respiratory and cardiac 1st harmonic power [0.59 ± 0.78], suggesting respiration can be the primary regulator of CSF depending on the individual differences in breathing techniques. Further work is needed to investigate the impact of sustained training yogic breathing on pulsatile CSF dynamics for CNS health.
Subclinical infection occurs frequently following low dose exposure to prions by blood transfusion
Authors: Salamat M. Khalid F. , Stewart Paula , Brown Helen , Tan Kyle B. C. , Smith Allister , de Wolf Christopher , Alejo Blanco A. Richard , Turner Marc , Manson Jean C. , McCutcheon Sandra , Houston E. Fiona 
Published: June 2022

AbstractInfectious prion diseases have very long incubation periods, and the role that subclinical infections play in transmission, persistence and re-emergence of these diseases is unclear. In this study, we used a well-established model of vCJD (sheep experimentally infected with bovine spongiform encephalopathy, BSE) to determine the prevalence of subclinical infection following exposure by blood transfusion from infected donors. Many recipient sheep survived for years post-transfusion with no clinical signs and no disease-associated PrP (PrPSc) found in post mortem tissue samples by conventional tests. Using a sensitive protein misfolding cyclic amplification assay (PMCA), we found that the majority of these sheep had detectable PrPSc in lymph node samples, at levels approximately 105–106 times lower than in equivalent samples from clinically positive sheep. Further testing revealed the presence of PrPSc in other tissues, including brain, but not in blood samples. The results demonstrate that subclinical infection is a frequent outcome of low dose prion infection by a clinically relevant route for humans (blood transfusion). The long term persistence of low levels of infection has important implications for prion disease control and the risks of re-emergent infections in both humans and animals.
Ab initio molecular dynamics free energy study of enhanced copper (II) dimerization on mineral surfaces
Authors: Leung Kevin , Greathouse Jeffery A. 
Published: June 2022

AbstractUnderstanding the adsorption of isolated metal cations from water on to mineral surfaces is critical for toxic waste retention and cleanup in the environment. Heterogeneous nucleation of metal oxyhydroxides and other minerals on material surfaces is key to crystal growth and dissolution. The link connecting these two areas, namely cation dimerization and polymerization, is far less understood. In this work we apply ab initio molecular dynamics calculations to examine the coordination structure of hydroxide-bridged Cu(II) dimers, and the free energy changes associated with Cu(II) dimerization on silica surfaces. The dimer dissociation pathway involves sequential breaking of two Cu2+-OH− bonds, yielding three local minima in the free energy profiles associated with 0-2 OH− bridges between the metal cations, and requires the design of a (to our knowledge) novel reaction coordinate for the simulations. Cu(II) adsorbed on silica surfaces are found to exhibit stronger tendency towards dimerization than when residing in water. Cluster-plus-implicit-solvent methods yield incorrect trends if OH− hydration is not correctly depicted. The predicted free energy landscapes are consistent with fast equilibrium times (seconds) among adsorbed structures, and favor Cu2+ dimer formation on silica surfaces over monomer adsorption.
Multimodal data integration using machine learning improves risk stratification of high-grade serous ovarian cancer
Authors: Boehm Kevin M. , Aherne Emily A. , Ellenson Lora , Nikolovski Ines , Alghamdi Mohammed , Vázquez-García Ignacio , Zamarin Dmitriy , Long Roche Kara , Liu Ying , Patel Druv , Aukerman Andrew , Pasha Arfath , Rose Doori , Selenica Pier , Causa Andrieu Pamela I. , Fong Chris , Capanu Marinela , Reis-Filho Jorge S. , Vanguri Rami , Veeraraghavan Harini , Gangai Natalie , Sosa Ramon , Leung Samantha , McPherson Andrew , Gao JianJiong ,   MSK MIND Consortium, Lakhman Yulia , Shah Sohrab P. 
Published: June 2022

AbstractPatients with high-grade serous ovarian cancer suffer poor prognosis and variable response to treatment. Known prognostic factors for this disease include homologous recombination deficiency status, age, pathological stage and residual disease status after debulking surgery. Recent work has highlighted important prognostic information captured in computed tomography and histopathological specimens, which can be exploited through machine learning. However, little is known about the capacity of combining features from these disparate sources to improve prediction of treatment response. Here, we assembled a multimodal dataset of 444 patients with primarily late-stage high-grade serous ovarian cancer and discovered quantitative features, such as tumor nuclear size on staining with hematoxylin and eosin and omental texture on contrast-enhanced computed tomography, associated with prognosis. We found that these features contributed complementary prognostic information relative to one another and clinicogenomic features. By fusing histopathological, radiologic and clinicogenomic machine-learning models, we demonstrate a promising path toward improved risk stratification of patients with cancer through multimodal data integration.
Symptomatic lithospheric drips triggering fast topographic rise and crustal deformation in the Central Andes
Authors: Andersen Julia , Göğüş Oguz H. , Pysklywec Russell N. , Santimano Tasca , Şengül Uluocak Ebru 
Published: June 2022

AbstractThe basin and plateau regions of the Central Andes have undergone phases of rapid subsidence and uplift during the last ~20 Myr in addition to internal tectonic deformation. Paleoelevation data and the presence of high seismic wave speed anomalies beneath the Puna Plateau suggest that these tectonic events may be related to lithospheric foundering. Here, we study the geodynamic processes in the region using three dimensional, scaled, analogue models and high-resolution optical image correlation techniques. The analogue experiments show how a gravitational instability of the mantle lithosphere developing into a lithospheric drip may form a circular sedimentary basin in the crust that undergoes subsidence and subsequently reverses to uplift, while simultaneously undergoing internal crustal shortening. The model results reveal that drips may be “symptomatic” where the crust is well coupled to the sinking mantle lithosphere and manifests tectonic deformation at the surface, or poorly coupled “asymptomatic” drips with weak crustal surface manifestations. Overall, the physical models suggest that the formation of the Arizaro Basin and nearby Central Andean basins are caused by symptomatic lithospheric dripping events and highlight the significant role of non-subduction geodynamic mechanisms in driving surface tectonics.
Leveraging genomics to understand the broader role of fungal small secreted proteins in niche colonization and nutrition
Authors: Plett Jonathan M , Plett Krista L 
Published: June 2022

Abstract
The last few years have seen significant advances in the breadth of fungi for which we have genomic resources and our understanding of the biological mechanisms evolved to enable fungi to interact with their environment and other organisms. One field of research that has seen a paradigm shift in our understanding concerns the role of fungal small secreted proteins (SSPs) classified as effectors. Classically thought to be a class of proteins utilized by pathogenic microbes to manipulate host physiology in support of colonization, comparative genomic studies have demonstrated that mutualistic fungi and fungi not associated with a living host (i.e., saprotrophic fungi) also encode inducible effector and candidate effector gene sequences. In this review, we discuss the latest advances in understanding how fungi utilize these secreted proteins to colonize a particular niche and affect nutrition and nutrient cycles. Recent studies show that candidate effector SSPs in fungi may have just as significant a role in modulating hyphosphere microbiomes and in orchestrating fungal growth as they do in supporting colonization of a living host. We conclude with suggestions on how comparative genomics may direct future studies seeking to characterize and differentiate effector from other more generalized functions of these enigmatic secreted proteins across all fungal lifestyles.