bluuebunny/crossref_metadata_2025 huggingface dataset:
Biomimicry: Function and Aesthetic of Vacation Home, Chonburi
Authors: Techaborikiti Suparuek
Published: September 2021

The aim of this research is to look into the architecture world today where sustainability and energy consumption are a new trend of urban architecture. The interpretation of biomimicry architecture that involving in biocentric world. The differentiation of biomimicry and biomorphic led to my extrapolate of the decision in understanding between the two. The understanding of biomorphic versus biomimicry is that biomorphic only form that resemble of nature however, biomimicry is the function that adapt through the study of function of nature. Moreover, because biomimicry takes root from nature itself, the adaptation is not too alien to environment built and can achieve the outcome equal or toward energy consumption and sustainability. Introducing project of biomimicry in Chonburi [1] to provide a new architecture design for vacation home in the area for a new way of sustainability living and invitation to new economy attraction to tourists in Thailand. With the analytical to identify the problem in Chonburi where the province ranked number two in Gross Provincial Product (GPP) according to GPP Analysis from TERRABKK. This research study focuses on the combination of function of biomimicry in architecture and architectural aesthetic. The research topic is to study environmental, climate, and site analysis to find the equilibrium price of the area and construction materials that can be found within the area for the design.
Metamorphic Evolution of Calc-silicate Body Enclosed in Charnockitic Gneiss at West Ongul Island, Lützow-Holm Complex, East Antarctica
Authors: Thaworndumrongsakul Penchan , Booth John , Nantasin Prayath , Kim Yoonsup
Published: September 2021

This paper provides a report of a study of a series of boudined bodies of mineralogically zoned calc-silicate bodies, some over 1 m thick, enclosed in granulite facies charnockitic gneisses on West Ongul Island, Lützow-Holm Complex, East Antarctica. Zircons extracted from the centre of one of the calc-silicate bodies indicate that they were metamorphosed around 532.3 ± 0.8 Ma and that the cores of these zircons were inherited from igneous rocks intruded 738.5 ± 1.8 Ma and possibly 605.0 ± 1.2 Ma. The meionite content of scapolite indicates that the peak metamorphic temperature reached a minimum of 790 °C. In the outermost rim of the calc-silicate scapolite is partially replaced by clinopyroxene, probably as a result of the influx of Mg bearing fluids from the surrounding charnockite gneiss during uplift and decompression. An influx of hydrous fluid resulted in the almost complete retrogressive alteration of plagioclase to sericite throughout the calc-silicates, with minor growth of amphibole after clinopyroxene and calcite after scapolite only in the innermost zone.
Interpretation of the apparent activation energy of glass transition
Authors: Shirai Koun
Published: September 2021

The temperature dependence of the viscosity of glass is a major concern in glass research. The apparent activation energies obtained from Arrhenius plots often show unusual values larger than bond energies, which makes the interpretation of the activation energy difficult. In this study, a reasonable interpretation of the apparent activation energy is obtained along similar lines as those adopted in solid state physics and chemistry. In contrast to the widely held view that the transition occurs at the reference temperature T
0 according to the Vogel–Fulcher–Tammann formula, in this work the structural change observed at the calorimetric temperature T

g
is considered as a transition from the liquid to solid phases. The energy barrier for atom rearrangements significantly changes in the transition range with width ΔT

g
. This change in the energy barrier alters the manner in which the apparent activation energy constitutes the Arrhenius form. Analysis of available experimental data shows that the real value of energy barrier is significantly smaller than the apparent activation energy, and the obtained values are in the reasonable range of energy expected for chemical bonds. The overestimation of the apparent activation energy depends on the ratio T

g
/ΔT

g
, which is larger for fragile glasses than for strong glasses. Importantly, the linear term in the temperature dependence of the energy barrier does not appear in Arrhenius plots. This explains why the temperature dependence of viscosity for strong glasses obeys well the Arrhenius law, despite that the temperature dependence of energy barrier is expected for every glass.
Neutron studies of Na-ion battery materials
Authors: Shah Ami R , Shutt Rebecca R C , Smith Keenan , Hack Jennifer , Neville Tobias P , Headen Thomas F , Brett Dan J L , Howard Christopher A , Miller Thomas S , Cullen Patrick L
Published: September 2021

The relative vast abundance and more equitable global distribution of terrestrial sodium makes sodium-ion batteries (NIBs) potentially cheaper and more sustainable alternatives to commercial lithium-ion batteries (LIBs). However, the practical capacities and cycle lives of NIBs at present do not match those of LIBs and have therefore hindered their progress to commercialisation. The present drawback of NIB technology stems largely from the electrode materials and their associated Na+ ion storage mechanisms. Increased understanding of the electrochemical storage mechanisms and kinetics is therefore vital for the development of current and novel materials to realise the commercial NIB. In contrast to x-ray techniques, the non-dependency of neutron scattering on the atomic number of elements (Z) can substantially increase the scattering contrast of small elements such as sodium and carbon, making neutron techniques powerful for the investigation of NIB electrode materials. Moreover, neutrons are far more penetrating which enables more complex sample environments including in situ and operando studies. Here, we introduce the theory of, and review the use of, neutron diffraction and quasi-elastic neutron scattering, to investigate the structural and dynamic properties of electrode and electrolyte materials for NIBs. To improve our understanding of the actual sodium storage mechanisms and identify intermediate stages during charge/discharge, ex situ, in situ, and operando neutron experiments are required. However, to date there are few studies where operando experiments are conducted during electrochemical cycling. This highlights an opportunity for research to elucidate the operating mechanisms within NIB materials that are under much debate at present.
Anomalous diffusion in the citation time series of scientific publications
Authors: Zamani Maryam , Aghion Erez , Pollner Peter , Vicsek Tamas , Kantz Holger
Published: September 2021

We analyze the citation time-series of manuscripts in three different fields of science; physics, social science and technology. The evolution of the time-series of the yearly number of citations, namely the citation trajectories, diffuse anomalously, their variance scales with time ∝t
2H
, where H ≠ 1/2. We provide detailed analysis of the various factors that lead to the anomalous behavior: non-stationarity, long-ranged correlations and a fat-tailed increment distribution. The papers exhibit a high degree of heterogeneity across the various fields, as the statistics of the highest cited papers is fundamentally different from that of the lower ones. The citation data is shown to be highly correlated and non-stationary; as all the papers except the small percentage of them with high number of citations, die out in time.
Model-free control of dynamical systems with deep reservoir computing
Authors: Canaday Daniel , Pomerance Andrew , Gauthier Daniel J
Published: September 2021

We propose and demonstrate a nonlinear control method that can be applied to unknown, complex systems where the controller is based on a type of artificial neural network known as a reservoir computer. In contrast to many modern neural-network-based control techniques, which are robust to system uncertainties but require a model nonetheless, our technique requires no prior knowledge of the system and is thus model-free. Further, our approach does not require an initial system identification step, resulting in a relatively simple and efficient learning process. Reservoir computers are well-suited to the control problem because they require small training data sets and remarkably low training times. By iteratively training and adding layers of reservoir computers to the controller, a precise and efficient control law is identified quickly. With examples on both numerical and high-speed experimental systems, we demonstrate that our approach is capable of controlling highly complex dynamical systems that display deterministic chaos to nontrivial target trajectories.
The Role of Experiments in Monarch Butterfly Conservation: A Review of Recent Studies and Approaches
Authors: Pocius Victoria M , Majewska Ania A , Freedman Micah G
Published: September 2021

Monarch butterflies (Danaus plexippus) (Lepidoptera Danaidae Danaus plexippus (Linnaeus)) are an iconic species of conservation concern due to declines in the overwintering colonies over the past twenty years. Because of this downward trend in overwintering numbers in both California and Mexico, monarchs are currently considered ‘warranted-but-precluded’ for listing under the Endangered Species Act. Monarchs have a fascinating life history and have become a model system in chemical ecology, migration biology, and host–parasite interactions, but many aspects of monarch biology important for informing conservation practices remain unresolved. In this review, we focus on recent advances using experimental and genetic approaches that inform monarch conservation. In particular, we emphasize three areas of broad importance, which could have an immediate impact on monarch conservation efforts: 1) breeding habitat and host plant use, 2) natural enemies and exotic caterpillar food plants, and 3) the utility of genetic and genomic approaches for understanding monarch biology and informing ongoing conservation efforts. We also suggest future studies in these areas that could improve our understanding of monarch behavior and conservation.
Do we AGREE on the targets of antihypertensive drug treatment in older adults: a systematic review of guidelines on primary prevention of cardiovascular diseases
Authors: Bogaerts Jonathan M K , von Ballmoos Leonie M , Achterberg Wilco P , Gussekloo Jacobijn , Streit Sven , van der Ploeg Milly A , Drewes Yvonne M , Poortvliet Rosalinde K E
Published: September 2021

Background

translation of the available evidence concerning primary cardiovascular prevention into clinical guidance for the heterogeneous population of older adults is challenging. With this review, we aimed to give an overview of the thresholds and targets of antihypertensive drug therapy for older adults in currently used guidelines on primary cardiovascular prevention. Secondly, we evaluated the relationship between the advised targets and guideline characteristics, including guideline quality.

Methods

we systematically searched PubMed, Embase, Emcare and five guideline databases. We selected guidelines with (i) numerical thresholds for the initiation or target values of antihypertensive drug therapy in context of primary prevention (January 2008–July 2020) and (ii) specific advice concerning antihypertensive drug therapy in older adults. We extracted the recommendations and appraised the quality of included guidelines with the AGREE II instrument.

Results

thirty-four guidelines provided recommendations concerning antihypertensive drug therapy in older adults. Twenty advised a higher target of systolic blood pressure (SBP) for octogenarians in comparison with the general population and three advised a lower target. Over half of the guidelines (n = 18) recommended to target a SBP <150 mmHg in the oldest old, while four endorsed targets of SBP lower than 130 or 120 mmHg. Although many guidelines acknowledged frailty, only three gave specific thresholds and targets. Guideline characteristics, including methodological quality, were not related with the recommended targets.

Conclusion

the ongoing debate concerning targets of antihypertensive treatment in older adults, is reflected in an inconsistency of recommendations across guidelines. Recommended targets are largely set on chronological rather than biological age.
Long-term conditions, multimorbidity, lifestyle factors and change in grip strength over 9 years of follow-up: Findings from 44,315 UK biobank participants
Authors: Hurst Christopher , Murray James C , Granic Antoneta , Hillman Susan J , Cooper Rachel , Sayer Avan Aihie , Robinson Sian M , Dodds Richard M
Published: September 2021

Background

Weak grip strength is associated with a range of adverse health outcomes and an accelerated decline in grip strength confers an even greater risk. The factors associated with change in grip strength in mid-life remain to be fully determined.

Methods

We used data from 44,315 UK Biobank participants who had grip strength measured at baseline (2006-10) and a subsequent visit approximately nine years later. At baseline, participants’ long-term conditions (LTCs) were categorised against a hierarchy, with multimorbidity characterised by the number of LTC categories. Lifestyle factors were assessed. Change in grip strength was grouped into four patterns: decline, stable low, stable high or reference (no change or increase) and used as the outcome in multinomial logistic regression.

Results

Most LTC categories were associated with adverse patterns of change in grip strength (stable low and/or decline): for example, musculoskeletal/trauma conditions were associated with an increased risk of the stable low pattern (Relative Risk Ratio [RRR] = 1.63; 95% confidence interval [CI]: 1.49-1.79). Multimorbidity and lifestyle factors had independent associations with grip strength change. Those with 3+ categories of LTCs were more likely to experience decline in grip strength (RRR = 1.18; 95% CI: 1.08-1.28) compared to those with none. Low physical activity was associated with adverse patterns of grip strength, while raised body mass index (BMI) had divergent associations.

Conclusions

Individuals living with multimorbidity and those with lifestyle risk factors such as low physical activity are at increased risk of low muscle strength and the loss of strength over time.
Necrotising fasciitis: clinical judgement and early multidisciplinary collaboration is the key
Authors: Hosty Jennifer , Cheema Ali , Magdum Ashish A
Published: September 2021

Necrotising fasciitis is a bacterial infection of subcutaneous tissue and fascia, which can rapidly progress to septic shock. Diagnosis is frequently delayed or missed due to non-specific presentation. The laboratory risk indicator for necrotising fasciitis (LRINEC) stratifies risk based on biochemical results, but external validation revealed limited accuracy.

A 78-year-old female with significant co-morbidities presented with right foot pain and erythema. Vital signs were normal and C-reactive protein was 18 mg/l. LNIREC was 0. She was treated for cellulitis, but within 24 h developed skin blistering and necrosis. After consideration of risks, washout and debridement was performed under popliteal block. Recovery was prolonged and complicated by nosocomial infection. This case highlights the importance of clinical suspicion for necrotising fasciitis and the complexity of management decisions considering recovery can be protracted.
Olive oil consumption is associated with lower frailty risk: a prospective cohort study of community-dwelling older adults
Authors: Donat-Vargas Carolina , Domínguez Ligia J , Sandoval-Insausti Helena , Moreno-Franco Belén , Rey-Garcia Jimena , Banegas José R , Rodríguez-Artalejo Fernando , Guallar-Castillón Pilar
Published: September 2021

Background

There is no evidence on the specific beneficial association of the main types of olive oil consumption with frailty.

Objective

The aim was to assess the relationship between olive oil consumption and incident frailty in community-dwelling older adults.

Design

Prospective cohort.

Setting

Participants were recruited in 2008–10 and follow-up through 2013.

Subjects

In total, 1,896 older adults aged 60+.

Methods

At baseline, olive oil and other food consumption was collected using a validated dietary history. Incident frailty was defined as having at least three of the following five Fried-based criteria: low physical activity, fatigue, slow walking, muscle weakness and unintentional weight loss. Analyses were performed with logistic regression and adjusted for the major confounders.

Results

Over a mean follow-up of 3.5 years, 135 incident frailty cases were identified. The odds ratio (95% confidence interval) of frailty across sex-specific tertiles of total olive oil consumption (12.7, 20 and 30.8 g/day, respectively) were: 1 (ref.), 0.52 (0.32, 0.83) and 0.47 (0.29, 0.78), P trend 0.003. When differentiating by olive oil types, the results held for virgin but did not for common (refined) olive oil.

Conclusion

The highest total olive oil consumption (~3 tablespoons), especially if virgin, was associated with half the risk of frailty as the lowest consumption (~1 tablespoon) among older adults. This study suggests that virgin olive oil should be the preferent culinary olive oil type for frailty prevention. If confirmed in other settings, small doses of virgin olive oil could be added as a simple geriatric nutritional advice on the prevention of frailty.
The Wages of Harlotry—Luise White’s The Comforts of Home: Prostitution in Colonial Nairobi (1990–2020)
Authors: Mutongi Kenda
Published: September 2021

In “The Wages of Harlotry,” Kenda Mutongi examines the historiographical significance of Luise White’s The Comforts of Home: Prostitution in Colonial Nairobi (1990). She argues that White’s main contribution has been connecting the history of prostitution in Nairobi to histories of family, labor, sexuality, gender, colonial state, housing, urban life, and political economy—that is, White is a pioneer in writing entangled, layered, and intersectional histories that have an enduring influence today despite early skepticism about her work. Drawing partly on scholars’ solicited reminiscences of teaching and reading the book, Mutongi shows that White has been a fierce feminist and a fascinatingly eclectic African historian. To fully understand the influence of White’s book, Mutongi argues, we have to go beyond what we read between its covers and talk with people who lived and worked with White while she was researching and writing the book as well as those who have taught it to different generations of students over the last thirty years.
Freedom with Local Bonds: Custom and Manumission in the Age of Emancipation
Authors: Chira Adriana
Published: September 2021

Throughout the first half of the nineteenth century, across Latin America, expansive rural communities of African descent forged freedom from below in the shadows of highly exploitative extractive economies. Their efforts push us to reconsider established genealogies of the age of emancipation. Freedom through conditional manumission and enslaved people’s reliance on social networks to obtain it opened the door to custom inside first-instance district courts in such areas. Judges turned to vernacular understandings of rights and obligations as they clarified the ambiguous statuses of the conditionally freed for which written law offered few provisions. Through manumission and legal actions to defend freedom, peasants of African descent on the margins of the global economic system grounded their rights in state structures as local custom. Black freedom within such territories represents a mode of community governance that remains invisible if studied by focusing on mobility or nation building. Seen from a place such as Santiago de Cuba, the nineteenth century was not just a time when Africans and Afro-descendants pursued social inclusion through ideologies of national citizenship and diasporic connections. It was also a time of freedom through membership in local communities, which women and families were especially instrumental in forging.
Capitulations Redux: The Imperial Genealogy of the Post–World War I “Minority” Regimes
Authors: Robson Laura
Published: September 2021

Scholars have long considered the post–World War I minorities regime—defined and encompassed by a series of “minorities treaties” with various Balkan, Eastern European, and Middle Eastern states and the construction of a “Minorities Commission” in the new League of Nations to enforce them—as a basically well-intentioned, if ultimately misguided, first step toward the concept of internationally guaranteed human rights. In fact, the minorities treaties had vanishingly little to do with European concern for actual minority populations anywhere. Rather, they represented a new iteration of an imperial vision that had marked relations between the Ottoman Empire and the European powers of Britain, France, and Russia since the late eighteenth century: the idea, enshrined in the so-called capitulations agreements, that non-Muslim communities within the Ottoman sphere could represent a site of European economic, political, and military intervention and redefine the Ottoman state—and now the emerging nation-states of Eastern Europe, the Balkans, Anatolia, and the Levant—as possessing a lesser form of sovereignty.
VS38c and CD38-Multiepitope Antibodies Provide Highly Comparable Minimal Residual Disease Data in Patients With Multiple Myeloma
Authors: Broijl Annemiek , de Jong Augustinus C M , van Duin Mark , Sonneveld Pieter , Kühnau Jesper , van der Velden Vincent H J
Published: September 2021

Objectives

To compare flow cytometric minimal residual disease (MRD) data obtained using the EuroFlow approach, including the CD38-multiepitope (ME) antibody or the VS38c antibody.

Methods

We evaluated 29 bone marrow samples from patients with multiple myeloma (MM), of whom 15 had received daratumumab within the past 6 months. We evaluated MRD data and fluorescence intensities.

Results

Qualitative MRD data were 100% concordant between the 2 approaches. In MRD-positive samples (n = 14), MRD levels showed an excellent correlation (R2 = 0.999). Whereas VS38c staining was strong in both normal plasma cells and MM cells, independent of daratumumab treatment, staining intensities for CD38 were lower in MM cells compared with normal plasma cells, and on both cell types CD38 expression was significantly reduced in daratumumab-treated patients.

Conclusions

Both CD38-ME and VS38c allow reliable MRD detection in MM patients, but the high expression of VS38c allows easier identification of MM cells, especially in daratumumab-treated patients.
Expanding the Spectrum of Adult NTRK3-Rearranged Spindle Cell Neoplasms: A Recurrent NTRK3-SQSTM1 Fusion Spindle Cell Tumor With Deceptively Bland Morphology
Authors: Punjabi Lavisha S , Sittampalam Kesavan
Published: September 2021

Objectives

NTRK-rearranged spindle cell neoplasms (other than infantile fibrosarcoma) are an emerging entity of tumors that demonstrate wide variation in clinical and histopathologic features. We report a case of an NTRK-rearranged spindle cell neoplasm bearing a deceptively bland morphology.

Methods

We performed histopathologic, immunohistochemical, and molecular evaluation on resection tissue. We also conducted a literature review on adult NTRK3-rearranged spindle cell neoplasms.

Results

The tumor presented as a recurrent ankle mass in an elderly patient. Histologically, it was composed of bland spindle cells set in a fibrous to edematous stroma. Blood vessels were interspersed with subtle perivascular hyalinization and scattered lymphoid aggregates. Immunohistochemically, the spindle cells expressed CD34 and S100 while being negative for SOX10. The tumor also showed cytoplasmic reactivity for pan–tyrosine receptor kinase immunohistochemistry. Next-generation sequencing identified an NTRK3-SQSTM1 fusion. To the best of our knowledge, this fusion pair has not been previously reported in adult NTRK-rearranged mesenchymal tumors.

Conclusions

Altogether, this rare and diagnostically challenging case of an NTRK3-rearranged spindle cell tumor with low-grade morphology is in contrast to many of the reported adult NTRK3-rearranged mesenchymal tumors. Recognition of low-grade NTRK-rearranged tumors demands close attention to clues in morphology and immunoprofiles.
Laboratory Predictors of Hemolytic Anemia in Patients With Systemic Loxoscelism
Authors: Jacobs Jeremy W , Bastarache Lisa , Thompson Mary Ann
Published: September 2021

Objectives

To develop a sensitive and specific protocol for detecting preclinical hemolysis in patients with brown recluse spider (BRS) bites by comparing a large cohort of individuals with brown recluse spider (BRS) bites with and without hemolytic anemia.

Methods

A cross-sectional, retrospective analysis of clinical features and laboratory values, including urinalysis (UA) and peripheral blood results, and timing of positive laboratory values prior to a significant drop in hematocrit was performed to evaluate effective predictors of clinically significant hemolysis.

Results

In total, 275 patients with BRS bites were identified (64 with hemolytic anemia). Sensitivity and specificity of UA positive for blood (with and without microscopic hematuria) for detecting hemolysis were 72% and 75%, respectively. The combination of elevated serum total bilirubin (TB) and lactate dehydrogenase (LDH) had greater sensitivity (94%) and specificity (91%) for detecting patients developing hemolysis. When TB and LDH were evaluated prior to a significant decrease in hematocrit, they were positive in 82% of cases, while UA was positive for blood prior to a hematocrit decrease in 38% of cases.

Conclusions

Serum TB and LDH levels are more effective at detecting preclinical hemolysis than UA and should be serially analyzed to triage patients with BRS bites before life-threatening hemolysis occurs.
Racial/Ethnic Differences in Actigraphy, Questionnaire, and Polysomnography Indicators of Healthy Sleep: The Multi-Ethnic Study of Atherosclerosis
Authors: Chung Joon , Goodman Matthew , Huang Tianyi , Wallace Meredith L , Johnson Dayna A , Bertisch Suzanne , Redline Susan
Published: September 2021

We utilized the comprehensive sleep assessment of the Multi-Ethnic Study of Atherosclerosis (2010–2013), a cohort of US White, Black, Chinese, and Hispanic adults and older adults (n = 1,736; mean age = 68.3 years), to draw 13 sleep dimensions and create composite Sleep Health Scores to quantify multidimensional sleep health disparities. After age and sex adjustment in linear regression, compared with White participants, Black participants showed the greatest global sleep disparity, followed by Hispanic and Chinese participants. We estimated relative “risk” (RR) of obtaining favorable sleep compared with White adults at the component level according to race/ethnicity (lower is worse). The largest disparities were in objectively measured sleep timing regularity (RRBlack = 0.37, 95% confidence interval (CI): 0.29, 0.47; RRHispanic = 0.64, 95% CI: 0.52, 0.78; RRChinese = 0.70, 95% CI: 0.54, 0.90) and duration regularity (RRBlack = 0.55, 95% CI: 0.47, 0.65; RRHispanic = 0.76, 95% CI: 0.66, 0.88; RRChinese = 0.74, 95% CI: 0.61, 0.90) after sex and age adjustment. Disparities in duration and continuity were also apparent, and Black adults were additionally disadvantaged in % slow-wave sleep (N3), sleepiness, and sleep timing (24-hour placement). Sleep timing regularity, duration regularity, duration, and continuity may comprise a multidimensional cluster of targets to reduce racial/ethnic sleep disparities.
Associations of Binge Drinking and Heavy Alcohol Use on Sugar and Fat Intake in a Cohort of Southern People Living with HIV
Authors: Rosen Erika M , Primeaux Stefany D , Simon Liz , Welsh David A , Molina Patricia E , Ferguson Tekeda F
Published: September 2021

Aims

To assess whether binge drinking and heavy alcohol use are associated with increased sugar and fat consumption among a Southern cohort of people living with HIV (PWH).

Methods

This was a cross-sectional analysis of PWH enrolled in the New Orleans Alcohol use in HIV (NOAH) Study (n = 215). Binge and heavy drinking were identified through a 30-day Alcohol Timeline-Followback and dietary intake was assessed through a 24-hour dietary recall.

Results

Participants were 65.4% male, 83.3% Black, with a mean age of 49.2 ± 9.9. Heavy drinkers consumed more total calories than abstainers (P = 0.035) and low-to-moderate drinkers (P = 0.024), and binge drinkers consumed more calories than non-binge drinkers (P = 0.025). Binge and heavy drinkers had significantly higher intake of total and saturated fat in grams. However, substantially increased caloric intake among these participants led to non-significant associations for alcohol use with high total and saturated fat intake as a percent of total energy intake (%TEI). Binge drinkers had lower odds of consuming high sugar as a %TEI (odds ratio: 0.31 [0.14, 0.68]). Additionally, sugar intake predicted total and saturated fat intake, and this association was slightly higher among binge drinkers (total fat P-value: 0.12).

Conclusions

In this population of PWH, while binge and heavy drinking predicted higher caloric and fat intake in grams, binge drinkers were less likely to consume a high-sugar diet. This analysis suggests that interventions focused on reduced alcohol use may be especially beneficial in reducing metabolic disease burden in PWH if supplemented with information on incorporating lower energy-dense foods with reduced fat.
Content externalism without thought experiments?
Authors: Morgan Jonathan Brink
Published: September 2021

A recent argument against content internalism bucks tradition: it abandons Twin-Earth-style thought experiments and instead claims that internalism is inconsistent with plausible principles relating belief contents and truth values. Call this (for reasons that will become obvious) the transparency argument. Here, it is shown that there is a structurally parallel argument against content internalism’s foil: content externalism. Preserving the transparency argument while fending off the parallel argument against externalism requires that (i) content-determination and truth-value-determination are implausibly linked together and that (ii) eternalism about belief contents is true. Given these requirements, there may be reason to prefer simple, thought-experiment-based arguments against internalism – the sort of arguments that the transparency argument is meant to supersede.
RhizoVision Explorer: open-source software for root image analysis and measurement standardization
Authors: Seethepalli Anand , Dhakal Kundan , Griffiths Marcus , Guo Haichao , Freschet Gregoire T , York Larry M
Published: September 2021

Roots are central to the function of natural and agricultural ecosystems by driving plant acquisition of soil resources and influencing the carbon cycle. Root characteristics like length, diameter and volume are critical to measure to understand plant and soil functions. RhizoVision Explorer is an open-source software designed to enable researchers interested in roots by providing an easy-to-use interface, fast image processing and reliable measurements. The default broken roots mode is intended for roots sampled from pots and soil cores, washed and typically scanned on a flatbed scanner, and provides measurements like length, diameter and volume. The optional whole root mode for complete root systems or root crowns provides additional measurements such as angles, root depth and convex hull. Both modes support providing measurements grouped by defined diameter ranges, the inclusion of multiple regions of interest and batch analysis. RhizoVision Explorer was successfully validated against ground truth data using a new copper wire image set. In comparison, the current reference software, the commercial WinRhizo™, drastically underestimated volume when wires of different diameters were in the same image. Additionally, measurements were compared with WinRhizo™ and IJ_Rhizo using a simulated root image set, showing general agreement in software measurements, except for root volume. Finally, scanned root image sets acquired in different labs for the crop, herbaceous and tree species were used to compare results from RhizoVision Explorer with WinRhizo™. The two software showed general agreement, except that WinRhizo™ substantially underestimated root volume relative to RhizoVision Explorer. In the current context of rapidly growing interest in root science, RhizoVision Explorer intends to become a reference software, improve the overall accuracy and replicability of root trait measurements and provide a foundation for collaborative improvement and reliable access to all.
Visual recognition and coevolutionary history drive responses of amphibians to an invasive predator
Authors: Melotto Andrea , Ficetola Gentile Francesco , Alari Elisa , Romagnoli Samuele , Manenti Raoul
Published: September 2021

During biotic invasions, native prey are abruptly exposed to novel predators and are faced with unprecedented predatory pressures. Under these circumstances, the lack of common evolutionary history may hamper predator recognition by native prey, undermining the expression of effective antipredator responses. Nonetheless, mechanisms allowing prey to overcome evolutionary naïveté exist. For instance, in naïve prey, history of coevolution with similar native predators or detection of general traits characterizing predators can favor the recognition of stimuli released by invasive predators. However, few studies have assessed how these mechanisms shape prey response at the community level. Here, we evaluated behavioral responses in naïve larvae of 13 amphibian species to chemical and visual cues associated with an invasive predator, the American red swamp crayfish (Procambarus clarkii). Moreover, we investigated how variation among species responses was related to their coexistence with similar native crayfish predators. Amphibian larvae altered their behavior in presence of visual stimuli of the alien crayfish, while chemical cues elicited feeble and contrasting behavioral shifts. Activity reduction was the most common and stronger response, whereas some species exhibited more heterogeneous strategies also involving distancing and rapid escape response. Interestingly, species sharing coevolutionary history with the native crayfish were able to finely tune their response to the invasive one, performing bursts to escape. These results suggest native prey can respond to invasive predators through recognition of generic risk cues (e.g., approaching large shapes), still the capability of modulating antipredator strategies may also depend on their coevolutionary history with similar native predators.
Population differences in the effect of context on personality in an invasive lizard
Authors: Brand Jack A , Naimo Annalise C , Michelangeli Marcus , Martin Jake M , Sih Andrew , Wong Bob B M , Chapple David G
Published: September 2021

Within populations, individuals often differ consistently in their average level of behavior (i.e., animal personality), as well as their response to environmental change (i.e., behavioral plasticity). Thus, changes in environmental conditions might be expected to mediate the structure of animal personality traits. However, it is currently not well understood how personality traits change in response to environmental conditions, and whether this effect is consistent across multiple populations within the same species. Accordingly, we investigated variation in personality traits across two ecological contexts in the invasive delicate skink (Lampropholis delicata). Specifically, lizards from three different populations were repeatedly measured for individual activity in group behavioral assays under differing levels of food availability. We found that environmental context had a clear effect on the structure of lizard personality, where activity rates were not repeatable in the absence of food, but were repeatable in the presence of food resources. The difference in repeatability of activity rates across contexts appeared to be largely driven by an increase in among-individual variance when tested in the presence of food resources. However, this was only true for one of the populations tested, with food context having no effect on the expression of personality traits in the other two populations. Our results highlight the important role of environmental context in mediating the structure of animal personality traits and suggest that this effect may vary among populations.
Condition-dependent sexual reproduction is driven by benefits, not costs of sex
Authors: Lever Jessica , Drapes Sally , Hall Matthew D , Booksmythe Isobel
Published: September 2021

Facultative sexual organisms must allocate resources to both asexual and sexual reproduction. Optimal patterns of investment in sex depend on the relative costs and benefits of each reproductive mode, and may consequently be context- and condition-dependent. Two proposed explanations for the observed variation in investment in sex among facultative sexual lineages invoke alternative condition-dependent scenarios. Under the fitness-associated sex hypothesis, sex is predicted when individuals are in poor condition or experience stressful environments. Under the resource-demanding sex hypothesis, sex is only affordable to individuals in good condition experiencing favourable environments. Direct tests of these contrasting hypotheses are rare; moreover, investment in different components of sexual reproduction responds differently to cues promoting sex, and may be subject to different energetic constraints. Using genotypes of facultative sexual Daphnia carinata that differ in their level of investment in sex, we manipulated resource availability while accounting for day length (a seasonal cue for sex) to evaluate these hypotheses. The sexual response to day length depended on resource availability: increased day lengths and reduced food availability increased the production of sexual eggs, and relative investment in males, in a manner consistent with the fitness-associated sex hypothesis. The pattern of condition-dependence was specific to each component of reproductive investment – while male production covaried with asexual fecundity across genotypes, increased sexual egg production was associated with reduced asexual reproduction. Our results suggest that investment in sex is determined largely by its context-dependent advantages, and that this investment is not moderated by immediate costs to asexual reproduction.
Conditional natal dispersal provides a mechanism for populations tracking resource pulses after fire
Authors: Stillman Andrew N , Lorenz Teresa J , Siegel Rodney B , Wilkerson Robert L , Johnson Matthew , Tingley Morgan W
Published: September 2021

Animals that persist in spatially structured populations face the challenge of tracking the rise and fall of resources across space and time. To combat these challenges, theory predicts that species should use conditional dispersal strategies that allow them to emigrate from patches with declining resources and colonize new resource patches as they appear. We studied natal dispersal movements in the black-backed woodpecker (Picoides arcticus), a species known for its strong association with recent post-fire forests in western North America. We radio-tracked juveniles originating from seven burned areas and tested hypotheses that environmental and individual factors influence dispersal distance and emigration rates—investigating emigration while additionally accounting for imperfect detection with a novel Bayesian model. We found that juveniles were more likely to leave natal areas and disperse longer distances if they were heavier or hatched in older burned areas where resources are increasingly scarce. Juveniles were also more likely to leave their natal burn if they hatched in a nest closer to the fire perimeter. While dispersing across the landscape, black-backed woodpeckers selected for burned forest relative to unburned available habitat. Together, these results strongly support the hypothesis that black-backed woodpecker populations track resource pulses across fire-prone landscapes, with conditional natal dispersal acting as a mechanism for locating and colonizing newly burned areas. Lending empirical support to theoretical predictions, our findings suggest that changes in resource distribution may shape dispersal patterns and, consequently, the distribution and persistence of spatially structured populations.
Assessing deep learning methods in cis-regulatory motif finding based on genomic sequencing data
Authors: Zhang Shuangquan , Ma Anjun , Zhao Jing , Xu Dong , Ma Qin , Wang Yan
Published: September 2021

Identifying cis-regulatory motifs from genomic sequencing data (e.g. ChIP-seq and CLIP-seq) is crucial in identifying transcription factor (TF) binding sites and inferring gene regulatory mechanisms for any organism. Since 2015, deep learning (DL) methods have been widely applied to identify TF binding sites and predict motif patterns, with the strengths of offering a scalable, flexible and unified computational approach for highly accurate predictions. As far as we know, 20 DL methods have been developed. However, without a clear and systematic assessment, users will struggle to choose the most appropriate tool for their specific studies. In this manuscript, we evaluated 20 DL methods for cis-regulatory motif prediction using 690 ENCODE ChIP-seq, 126 cancer ChIP-seq and 55 RNA CLIP-seq data. Four metrics were investigated, including the accuracy of motif finding, the performance of DNA/RNA sequence classification, algorithm scalability and tool usability. The assessment results demonstrated the high complementarity of the existing DL methods. It was determined that the most suitable model should primarily depend on the data size and type and the method’s outputs.
Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations
Authors: Wu Leyun , Peng Cheng , Yang Yanqing , Shi Yulong , Zhou Liping , Xu Zhijian , Zhu Weiliang
Published: September 2021

Although the current coronavirus disease 2019 (COVID-19) vaccines have been used worldwide to halt spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the emergence of new SARS-CoV-2 variants with E484K mutation shows significant resistance to the neutralization of vaccine sera. To better understand the resistant mechanism, we calculated the binding affinities of 26 antibodies to wild-type (WT) spike protein and to the protein harboring E484K mutation, respectively. The results showed that most antibodies (~85%) have weaker binding affinities to the E484K mutated spike protein than to the WT, indicating the high risk of immune evasion of the mutated virus from most of current antibodies. Binding free energy decomposition revealed that the residue E484 forms attraction with most antibodies, while the K484 has repulsion from most antibodies, which should be the main reason of the weaker binding affinities of E484K mutant to most antibodies. Impressively, a monoclonal antibody (mAb) combination was found to have much stronger binding affinity with E484K mutant than WT, which may work well against the mutated virus. Based on binding free energy decomposition, we predicted that the mutation of four more residues on receptor-binding domain (RBD) of spike protein, viz., F490, V483, G485 and S494, may have high risk of immune evasion, which we should pay close attention on during the development of new mAb therapeutics.
Representation of molecules for drug response prediction
Authors: An Xin , Chen Xi , Yi Daiyao , Li Hongyang , Guan Yuanfang
Published: September 2021

The rapid development of machine learning and deep learning algorithms in the recent decade has spurred an outburst of their applications in many research fields. In the chemistry domain, machine learning has been widely used to aid in drug screening, drug toxicity prediction, quantitative structure–activity relationship prediction, anti-cancer synergy score prediction, etc. This review is dedicated to the application of machine learning in drug response prediction. Specifically, we focus on molecular representations, which is a crucial element to the success of drug response prediction and other chemistry-related prediction tasks. We introduce three types of commonly used molecular representation methods, together with their implementation and application examples. This review will serve as a brief introduction of the broad field of molecular representations.
circRNA-binding protein site prediction based on multi-view deep learning, subspace learning and multi-view classifier
Authors: Li Hui , Deng Zhaohong , Yang Haitao , Pan Xiaoyong , Wei Zhisheng , Shen Hong-Bin , Choi Kup-Sze , Wang Lei , Wang Shitong , Wu Jing
Published: September 2021

Circular RNAs (circRNAs) generally bind to RNA-binding proteins (RBPs) to play an important role in the regulation of autoimmune diseases. Thus, it is crucial to study the binding sites of RBPs on circRNAs. Although many methods, including traditional machine learning and deep learning, have been developed to predict the interactions between RNAs and RBPs, and most of them are focused on linear RNAs. At present, few studies have been done on the binding relationships between circRNAs and RBPs. Thus, in-depth research is urgently needed. In the existing circRNA-RBP binding site prediction methods, circRNA sequences are the main research subjects, but the relevant characteristics of circRNAs have not been fully exploited, such as the structure and composition information of circRNA sequences. Some methods have extracted different views to construct recognition models, but how to efficiently use the multi-view data to construct recognition models is still not well studied. Considering the above problems, this paper proposes a multi-view classification method called DMSK based on multi-view deep learning, subspace learning and multi-view classifier for the identification of circRNA-RBP interaction sites. In the DMSK method, first, we converted circRNA sequences into pseudo-amino acid sequences and pseudo-dipeptide components for extracting high-dimensional sequence features and component features of circRNAs, respectively. Then, the structure prediction method RNAfold was used to predict the secondary structure of the RNA sequences, and the sequence embedding model was used to extract the context-dependent features. Next, we fed the above four views’ raw features to a hybrid network, which is composed of a convolutional neural network and a long short-term memory network, to obtain the deep features of circRNAs. Furthermore, we used view-weighted generalized canonical correlation analysis to extract four views’ common features by subspace learning. Finally, the learned subspace common features and multi-view deep features were fed to train the downstream multi-view TSK fuzzy system to construct a fuzzy rule and fuzzy inference-based multi-view classifier. The trained classifier was used to predict the specific positions of the RBP binding sites on the circRNAs. The experiments show that the prediction performance of the proposed method DMSK has been improved compared with the existing methods. The code and dataset of this study are available at https://github.com/Rebecca3150/DMSK.