bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative Analysis of Colonic Biopsies from Inflammatory Bowel Disease Patients Identifies an Interaction Between Microbial Bile Acid-inducible Gene Abundance and Human Angiopoietin-like 4 Gene Expression
Authors: Hernández-Rocha Cristian , Borowski Krzysztof , Turpin Williams , Filice Melissa , Nayeri Shadi , Raygoza Garay Juan Antonio , Stempak Joanne M , Silverberg Mark S 
Published: May 2021

AbstractBackground and AimsMicrobial-derived bile acids can modulate host gene expression, and their faecal abundance is decreased in active inflammatory bowel disease [IBD]. We analysed the impact of endoscopic inflammation on microbial genes involved in bile acid biotransformation, and their interaction with host transcriptome in the intestinal mucosa of IBD patients.MethodsEndoscopic mucosal biopsies were collected from non-inflamed and inflamed terminal ileum, ascending and sigmoid colon of IBD patients. Prediction of imputed metagenome functional content from 16S rRNA profile and real-time quantitative polymerase chain reaction [qPCR] were utsed to assess microbial bile acid biotransformation gene abundance, and RNA-seq was used for host transcriptome analysis. Linear regression and partial Spearman correlation accounting for age, sex, and IBD type were used to assess the association between microbial genes, inflammation, and host transcriptomics in each biopsy location. A Bayesian network [BN] analysis was fitted to infer the direction of interactions between IBD traits and microbial and host genes.ResultsThe inferred microbial gene pathway involved in secondary bile acid biosynthesis [ko00121 pathway] was depleted in inflamed terminal ileum of IBD patients compared with non-inflamed tissue. In non-inflamed sigmoid colon, the relative abundance of bile acid-inducible [baiCD] microbial genes was positively correlated with the host Angiopoietin-like 4 [Angptl4] gene expression. The BN analysis suggests that the microbial baiCD gene abundance could affect Angptl4 expression, and this interaction appears to be lost in the presence of inflammation.ConclusionsEndoscopic inflammation affects the abundance of crucial microbial bile acid-metabolising genes and their interaction with Angptl4 in intestinal mucosa of IBD patients.
Evaluating mobile health technologies: does the traditional randomized controlled trial serve our needs?
Authors: Gallagher Robyn , Zhang Ling 
Published: May 2021

Abstract
Mobile health technologies are increasingly used by cardiovascular nurses and allied health clinicians to support behaviour change and self-care in patients. Randomized controlled trials provide rigorous methodology for evaluation but progress slowly, so the technology is often outdated by completion. A helpful modification to the trial design includes identification of the behaviour intervention principles involved and concurrently track in-app usage data, allowing updates to be made. These data collected alongside user experiences enables analysis of effects on outcomes and determination of the relative influence of component parts. Cardiovascular and mental health mHealth strategies are used to exemplify these recommendations.
Establishment of spruce plantations in native birch forests reduces soil fungal diversity
Authors: Danielsen Jørgen Skyrud , Morgado Luis , Mundra Sunil , Nybakken Line , Davey Marie , Kauserud Håvard 
Published: May 2021

ABSTRACTPlantations of Norway spruce have been established well beyond its natural range in many parts of the world, potentially impacting native microbial ecosystems and the processes they mediate. In this study, we investigate how the establishment of spruce plantations in a landscape dominated by native birch forests in western Norway impacts soil properties and belowground fungal communities. Soil cores were collected from neighboring stands of planted spruce and native birch forests. We used DNA metabarcoding of the rDNA internal transcribed spacer 2 region and ergosterol measurements to survey the fungal community composition and its biomass, respectively. In the two investigated soil layers (litter and humus), fungal community composition, diversity and biomass were strongly affected by the tree species shift. Native birch stands hosted markedly richer fungal communities, including numerous fungi not present in planted spruce stands. In contrast, the spruce stands included higher relative abundance of ectomycorrhizal fungi as well as higher fungal biomass. Hence, establishing plantations of Norway spruce in native birch forests leads to significant losses in diversity, but increase in biomass of ectomycorrhizal fungi, which could potentially impact carbon sequestration processes and ecosystem functioning.
De novogenome assembly of the land snailCandidula unifasciata(Mollusca: Gastropoda)
Authors: Chueca Luis J , Schell Tilman , Pfenninger Markus 
Published: May 2021

AbstractAmong all molluscs, land snails are a scientifically and economically interesting group comprising edible species, alien species and agricultural pests. Yet, despite their high diversity, the number of genome drafts publicly available is still scarce. Here, we present the draft genome assembly of the land snail Candidula unifasciata, a widely distributed species along central Europe, belonging to the Geomitridae family, a highly diversified taxon in the Western-Palearctic region. We performed whole genome sequencing, assembly and annotation of an adult specimen based on PacBio and Oxford Nanopore long read sequences as well as Illumina data. A genome draft of about 1.29 Gb was generated with a N50 length of 246 kb. More than 60% of the assembled genome was identified as repetitive elements. In total, 22,464 protein-coding genes were identified in the genome, of which 62.27% were functionally annotated. This is the first assembled and annotated genome for a geometrid snail and will serve as reference for further evolutionary, genomic and population genetic studies of this important and interesting group.
Longitudinal Blood Pressure Patterns From Mid- to Late Life and Late-Life Hearing Loss in the Atherosclerosis Risk in Communities Study
Authors: Ting James , Jiang Kening , Du Simo , Betz Joshua , Reed Nicholas , Power Melinda C , Gottesman Rebecca , Sharrett A Richey , Griswold Michael , Walker Keenan A , Miller Edgar R , Lin Frank R , Deal Jennifer A 
Published: May 2021

Abstract

Background
Hearing loss is prevalent and associated with adverse functional outcomes in older adults. Prevention thus has far-reaching implications, yet few modifiable risk factors have been identified. Hypertension may contribute to age-related hearing loss, but epidemiologic evidence is mixed. We studied a prospective cohort of 3343 individuals from the Atherosclerosis Risk in Communities study, aged 44–65 years at baseline with up to 30 years of follow-up.

Methods
Hearing was assessed in late life (2016–2017) using a better-ear audiometric pure tone average (0.5, 1, 2, 4 kHz) and the Quick Speech-in-Noise (QuickSIN) test. Hypertension was defined as systolic blood pressure ≥140 mmHg, diastolic blood pressure ≥90 mmHg, or antihypertensive medication use. Midlife hypertension was defined by hypertension at 2 consecutive visits between 1987–1989 and 1996–1998. Late-life hypertension was defined in 2016–2017. Late-life low blood pressure was defined as a systolic blood pressure less than 90 mmHg or diastolic blood pressure less than 60 mmHg, irrespective of antihypertensive medication use. Associations between blood pressure patterns from mid- to late life and hearing outcomes were assessed using multivariable-adjusted linear regression.

Results
Compared to persistent normotension, persistent hypertension from mid- to late life was associated with worse central auditory processing (difference in QuickSIN score = −0.66 points, 95% CI: −1.14, −0.17) but not with audiometric hearing.

Conclusions
Participants with persistent hypertension had poorer late-life central auditory processing. These findings suggest that hypertension may be more strongly related to hearing-related changes in the brain than in the cochlea.
Increasing Faculty Involvement in the Undergraduate Interdisciplinary Learning Experience
Authors: Lent David D , Estes Korenna M , Hansen Alexandria K 
Published: May 2021

Synospis
More and more, we see that advances in life sciences are made because of Interdisciplinary collaborations. These collaborations are the future—they are necessary to solve the world’s most pressing problems and grand challenges. But are we preparing the next generation of scientists and the community for this future? At the University level, a number of initiatives and studies have suggested the need to reintegrate biology education and have made arguments that for students to build core competencies in biology, their education needs to be interdisciplinary. At the K-12 level, progress is being made to make learning interdisciplinary through the implementation of the Next-Generation Science Standards (NGSS). As NGSS is implemented, it will fundamentally change life sciences education at the K-12 level. However, when seeing the effect these initiatives and studies have had on the courses offered to students for their undergraduate biology degree, they still appear to be often siloed, with limited integration across disciplines. To make interdisciplinary biology education more successful, we need biologists, who for one reason or another have not been part of these conversations in the past and are more involved. We also need to increase communication and collaboration between biologists and educational researchers.
Pursuit and Evasion Strategies in the Predator–Prey Interactions of Fishes
Authors: Peterson Ashley N , Soto Alberto P , McHenry Matthew J 
Published: May 2021

SynopsisPredator–prey interactions are critical to the biology of a diversity of animals. Although prey capture is determined by the direction, velocity, and timing of motion by both animals, it is generally unclear what strategies are employed by predators and prey to guide locomotion. Here we review our research on fishes that tests the pursuit strategy of predators and the evasion strategy of prey through kinematic measurements and agent-based models. This work demonstrates that fish predators track prey with variations on a deviated-pursuit strategy that is guided by visual cues. Fish prey employ a mixed strategy that varies with factors such as the direction of a predator’s approach. Our models consider the stochastic nature of interactions by incorporating measured probability distributions to accurately predict measurements of survivorship. A sensitivity analysis of these models shows the importance of the response distance of prey to their survival. Collectively, this work demonstrates how strategy affects the outcome of predator–prey interactions and articulates the roles of sensing, control, and propulsion. The research program that we have developed has the potential to offer a framework for the study of strategy in the predator–prey interactions of a variety of animals.
Carbon management for savannah ecosystems in Central Africa: a case study from Cameroon
Authors: Awé Djongmo Victor , Noiha Noumi Valery , Zapfack Louis 
Published: May 2021

Abstract
The overall objective of this work is to assess the carbon sequestration potential and ecological service of savannah ecosystems in Cameroon. The destructive and non-destructive method was used to estimate the amount of carbon in different biomasses. The experimental setup used in this work is a random complete Fisher block device with four repetitions. The carbon stock in the aboveground biomass is ≥11.15 ± 2.41 tC/ha in the two regions. The carbon stock in litter biomass is ≥0.15 ± 0.02 tC/ha in the two regions. The carbon stock in herbaceous biomass is ≥3.00 ± 1.02 tC/ha in the savannah ecosystems within the regions. The carbon stock in dead wood biomass is ≥2.26 ± 1.09 tC/ha in the savannah ecosystems within regions. The carbon stock in the root biomass is ≥1.62 ± 0.18 tC/ha in the savannah ecosystems within the regions. Soil carbon stock is ≥3.74 ± 1.40 tC/ha in the two regions. The total carbon stocks ranged from 32.66 ± 3.05–71.06 ± 5.75 to 36.59 ± 3.50–69.85 ± 5.51 tC/ha in Adamawa and North regions, respectively. CO2 emissions are &gt;100 tCO2/ha in the savannah ecosystems within the regions. These results therefore confirm the contributing role of savannah ecosystems studied in the fight against the mitigation of climate change in the Adamawa and North region of Cameroon.
Hyperbolic Jigsaws and Families of Pseudomodular Groups II
Authors: Lou Beicheng , Tan Ser Peow , Vo Anh Duc 
Published: May 2021

Abstract
In our previous paper [ 5], we introduced a hyperbolic jigsaw construction and constructed infinitely many noncommensurable, nonuniform, non-arithmetic lattices of $\textrm{PSL}(2,{\mathbb R})$ with cusp set $\mathbb{Q} \cup \{\infty \}$ (called pseudomodular groups by Long and Reid [ 4]), thus answering a question posed by Long and Reid. In this paper, we continue with our study of these jigsaw groups exploring questions of arithmeticity, pseudomodularity, and also related pseudo-Euclidean and continued fraction algorithms arising from these groups. We also answer another question of Long and Reid [ 4] by demonstrating a recursive formula for the tessellation of the hyperbolic plane arising from Weierstrass groups, which generalizes the well-known “Farey addition” used to generate the Farey tessellation.
Kivy’s Mystery: Absolute Music and What the Formalist Can (or Could) Hear
Authors: Hagberg Garry L 
Published: May 2021

Abstract
Peter Kivy has said that the power of purely instrumental music remains an unexplained wonder. With this larger question in mind, I will consider: (1) the issues in musical aesthetics that led to what Kivy termed his enhanced formalism, (2) his conception of expressive properties in music and how a distinction between having and understanding an emotion can help clarify this issues here (that is, where what we gain in human understanding from having had the emotion is not contained within the experience of that emotion itself), and, most importantly for Kivy’s larger mystery, (3) the way that counterpoint, in an often unrecognized way, can present mimetic content of a kind that can explain the sense of musical profundity that it often awakens. It may turn out that absolute music’s profundity can be explained by the resonances this kind of layered and complex music has with the living, the ordering, the making sense, of a life.
Placental transfer of doravirine, a recent HIV-1 NNRTI in the ex vivo human cotyledon perfusion model
Authors: Lê Minh Patrick , Pencolé Lucile , Peytavin Gilles , Bouchet-Crivat Florian , Mandelbrot Laurent 
Published: May 2021

Abstract

Background
The recent HIV-1 NNRTI doravirine is likely to be used in pregnant women despite the complete lack of data on safety and exposure in the fetus. The objective of this study was to determine its placental transfer.

Methods
Maternal-to-fetal transfer was investigated using the open-circuit ex vivo dually perfused human cotyledon model. Doravirine was added to a maternal perfusate (theoretical doravirine concentration of 250 ng/mL) containing 2 g/L human albumin and 20 g/L antipyrine, a marker to validate the cotyledon’s viability, and cotyledons were dually perfused for up to 90 min.

Results
In five experiments, the median (IQR) doravirine concentrations in the maternal and fetal compartments were, respectively, 303 (178–420) and 40 (30–54) ng/mL, the fetal-to-maternal ratio was 16% (12%–18%) and the clearance index (in comparison with antipyrine transfer) was 48% (35%–64%). The median accumulation index in cotyledon tissue was 39% (range 10%–66%).

Conclusions
Doravirine both crosses and accumulates in the placenta. This may be useful as pre/post-exposure prophylaxis to reduce the risk of vertical HIV transmission but carries the potential for fetal toxicities. Further investigation is required to determine the safety and efficacy of this new antiretroviral agent in pregnancy.
Role of AzoR, a LysR-type transcriptional regulator, in SmeVWX pump-mediated antibiotic resistance in Stenotrophomonas maltophilia
Authors: Lu Hsu-Feng , Tsai Yu-Chieh , Li Li-Hua , Lin Yi-Tsung , Yang Tsuey-Ching 
Published: May 2021

Abstract

Background
The SmeVWX efflux pump of Stenotrophomonas maltophilia contributes to menadione (MD) tolerance and resistance to chloramphenicol, quinolones and tetracycline. The components of the SmeVWX efflux pump are encoded by a five-gene operon, smeU1VWU2X. We have previously demonstrated that the smeU1VWU2X operon is intrinsically unexpressed and inducibly expressed by MD via a SoxR- and SmeRv-involved regulatory circuit in S. maltophilia KJ. We also inferred that there should be other regulator(s) involved in MD-mediated smeU1VWU2X expression in addition to SoxR and SmeRv.

Objectives
To identify novel regulator(s) involved in the regulation of MD-mediated smeU1VWU2X expression and elucidate the regulatory circuit.

Methods
A possible regulator candidate involved in the regulation of MD-mediated smeU1VWU2X expression was identified by a homologue search using the helix-turn-helix domain of SmeRv as a query. Gene expression was assessed using the promoter-xylE transcriptional fusion assay and quantitative RT–PCR. The impact of the regulator on SmeVWX pump-mediated functions was investigated via mutant construction and functional tests (antibiotic susceptibility and MD tolerance).

Results
AzoR (Smlt3089), a LysR-type transcriptional regulator, was investigated. In unstressed logarithmically grown cells, AzoR was abundantly expressed and functioned as a repressor, inhibiting the expression of the smeU1VWU2X operon. MD challenge attenuated azoR expression, thus derepressing the expression of the smeU1VWU2X operon in S. maltophilia KJ. AzoR down-regulation-mediated smeU1VWU2X expression was observed in quinolone-resistant and SmeVWX-overexpressing S. maltophilia clinical isolates.

Conclusions
AzoR negatively regulates the expression of the smeU1VWU2X operon and SmeVWX pump-mediated antibiotic resistance in S. maltophilia.
Corn protein has greater concentrations of digestible amino acids and energy than low-oil corn distillers dried grains with solubles when fed to pigs but does not affect the growth performance of weanling pigs
Authors: Acosta Jessica P , Espinosa Charmaine D , Jaworski Neil W , Stein Hans H 
Published: May 2021

AbstractThree experiments were conducted to test the hypothesis that standardized ileal digestibility (SID) of amino acids (AA) and digestible energy (DE) and metabolizable energy (ME) in a new source of corn protein are greater than in corn distillers dried grains with solubles (DDGS) and that corn protein may be included in diets for weanling pigs. In experiment 1, the SID of AA was determined in two sources of DDGS (DDGS-1 and DDGS-2) and in corn protein. Results indicated that SID of most AA was greater (P &lt; 0.05) in DDGS-2 and corn protein than in DDGS-1, but corn protein contained more digestible AA than both sources of DDGS. In experiment 2, the DE and ME in corn, the two sources of DDGS, and corn protein were determined. Results demonstrated that DE (dry matter basis) in corn protein was greater (P &lt; 0.05) than in corn, but ME (dry matter basis) was not different between corn and corn protein. However, DE and ME in corn (dry matter basis) were greater (P &lt; 0.05) than in DDGS-1 and DDGS-2. In experiment 3, 160 weanling pigs were allotted to four treatments in phases 1 and 2 and a common diet in phase 3. Corn protein was included at 5% to 10% in phases 1 and 2 at the expense of plasma protein and enzyme-treated soybean meal. Results indicated that although differences in average daily gain and gain to feed ratio were observed in phase 1, no differences among treatments were observed for the overall experimental period. In conclusion, the concentration of digestible AA is greater in corn protein than in DDGS; DE and ME in corn protein are also greater than in DDGS; and up to 10% corn protein may be included in phase 1 and phase 2 diets for weanling pigs.
The Fat-glandular Interface and Breast Tumor Locations: Appearances on Ultrasound Tomography Are Supported by Quantitative Peritumoral Analyses
Authors: Littrup Peter J , Duric Nebojsa , Sak Mark , Li Cuiping , Roy Olivier , Brem Rachel F , Yamashita Mary 
Published: May 2021

Abstract

Objective
To analyze the preferred tissue locations of common breast masses in relation to anatomic quadrants and the fat-glandular interface (FGI) using ultrasound tomography (UST).

Methods
Ultrasound tomography scanning was performed in 206 consecutive women with 298 mammographically and/or sonographically visible, benign and malignant breast masses following written informed consent to participate in an 8-site multicenter, Institutional Review Board-approved cohort study. Mass locations were categorized by their anatomic breast quadrant and the FGI, which was defined by UST as the high-contrast circumferential junction of fat and fibroglandular tissue on coronal sound speed imaging. Quantitative UST mass comparisons were done for each tumor and peritumoral region using mean sound speed and percentage of fibroglandular tissue. Chi-squared and analysis of variance tests were used to assess differences.

Results
Cancers were noted at the FGI in 95% (74/78) compared to 51% (98/194) of fibroadenomas and cysts combined (P &lt; 0.001). No intra-quadrant differences between cancer and benign masses were noted for tumor location by anatomic quadrants (P = 0.66). Quantitative peritumoral sound speed properties showed that cancers were surrounded by lower mean sound speeds (1477 m/s) and percent fibroglandular tissue (47%), compared to fibroadenomas (1496 m/s; 65.3%) and cysts (1518 m/s; 84%) (P &lt; 0.001; P &lt; 0.001, respectively).

Conclusion
Breast cancers form adjacent to fat and UST localized the vast majority to the FGI, while cysts were most often completely surrounded by dense tissue. These observations were supported by quantitative peritumoral analyses of sound speed values for fat and fibroglandular tissue.
Unmet need for palliative rehabilitation in inpatient hospices/palliative care units: a nationwide post-bereavement survey
Authors: Hasegawa Takaaki , Akechi Tatsuo , Osaga Satoshi , Tsuji Tetsuya , Okuyama Toru , Sakurai Haruka , Masukawa Kento , Morita Tatsuya , Kizawa Yoshiyuki , Tsuneto Satoru , Shima Yasuo , Miyashita Mitsunori 
Published: May 2021

Abstract
In end-of-life care, rehabilitation for terminally ill cancer patients is inconsistently provided and rarely discussed. We sought to clarify the prevalence of unmet rehabilitation need for patients admitted to inpatient hospice/palliative care units as perceived by bereaved family members. We conducted a nationwide questionnaire survey of 1001 family members of cancer patients who died at inpatient hospices/palliative care units. For cancer patients who did not receive rehabilitation, we asked if family members perceived that the patient would have wanted rehabilitation intervention. Data were obtained from 416 respondents. Of these, 281 (67.5%) cases received no rehabilitation. The need for physical modalities was the most frequently reported (27.8%; 95% CI: 22.6–33.4), followed by relief of dyspnea (25.6%; 95% CI: 20.6–31.1) and treatment of edema (23.8%; 95% CI: 19.0–29.3). A non-negligible proportion of bereaved families reported unmet need for rehabilitation related to symptom management in inpatient hospices/palliative care units.