bluuebunny/crossref_metadata_2025_split huggingface dataset:
Understanding crown shyness from a 3-D perspective
Authors: van der Zee Jens , Lau Alvaro , Shenkin Alexander 
Published: February 2021

AbstractBackground and AimsCrown shyness describes the phenomenon whereby tree crowns avoid growing into each other, producing a puzzle-like pattern of complementary tree crowns in the canopy. Previous studies found that tree slenderness plays a role in the development of crown shyness. Attempts to quantify crown shyness have largely been confined to 2-D approaches. This study aimed to expand the current set of metrics for crown shyness by quantifying the characteristic of 3-D surface complementarity between trees displaying crown shyness, using LiDAR-derived tree point clouds. Subsequently, the relationship between crown surface complementarity and slenderness of trees was assessed.MethodsFourteen trees were scanned using a laser scanning device. Individual tree points clouds were extracted semi-automatically and manually corrected where needed. A metric that quantifies the surface complementarity (Sc) of a pair of protein molecules is applied to point clouds of pairs of adjacent trees. Then 3-D tree crown surfaces were generated from point clouds by computing their α shapes.Key ResultsTree pairs that were visually determined to have overlapping crowns scored significantly lower Sc values than pairs that did not overlap (n = 14, P &lt; 0.01). Furthermore, average slenderness of pairs of trees correlated positively with their Sc score (R2 = 0.484, P &lt; 0.01), showing agreement with previous studies on crown shyness.ConclusionsThe characteristic of crown surface complementarity present in trees displaying crown shyness was succesfully quantified using a 3-D surface complementarity metric adopted from molecular biology. Crown surface complementarity showed a positive relationship to tree slenderness, similar to other metrics used for measuring crown shyness. The 3-D metric developed in this study revealed how trees adapt the shape of their crowns to those of adjacent trees and how this is linked to the slenderness of the trees.
Changes in Severe Acute Respiratory Syndrome Coronavirus 2 Seroprevalence Over Time in 10 Sites in the United States, March–August, 2020
Authors: Lim Travis , Delorey Mark , Bestul Nicolette , Johannson Michael A , Reed Carrie , Hall Aron J , Fry Alicia M , Edens Chris , Semenova Vera , Li Han , Browning Peter , Desai Rita , Epperson Monica , Jia Tao , Thornburg Natalie J , Schiffer Jarad , Havers Fiona P 
Published: February 2021

Abstract

Background
Monitoring of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody prevalence can complement case reporting to inform more accurate estimates of SARS-CoV-2 infection burden, but few studies have undertaken repeated sampling over time on a broad geographic scale.

Methods
We performed serologic testing on a convenience sample of residual serum obtained from persons of all ages, at 10 sites in the United States from 23 March through 14 August 2020, from routine clinical testing at commercial laboratories. We standardized our seroprevalence rates by age and sex, using census population projections and adjusted for laboratory assay performance. Confidence intervals were generated with a 2-stage bootstrap. We used bayesian modeling to test whether seroprevalence changes over time were statistically significant.

Results
Seroprevalence remained below 10% at all sites except New York and Florida, where it reached 23.2% and 13.3%, respectively. Statistically significant increases in seroprevalence followed peaks in reported cases in New York, South Florida, Utah, Missouri, and Louisiana. In the absence of such peaks, some significant decreases were observed over time in New York, Missouri, Utah, and Western Washington. The estimated cumulative number of infections with detectable antibody response continued to exceed reported cases in all sites.

Conclusions
Estimated seroprevalence was low in most sites, indicating that most people in the United States had not been infected with SARS-CoV-2 as of July 2020. The majority of infections are likely not reported. Decreases in seroprevalence may be related to changes in healthcare-seeking behavior, or evidence of waning of detectable anti–SARS-CoV-2 antibody levels at the population level. Thus, seroprevalence estimates may underestimate the cumulative incidence of infection.
The ghosts of parasitism past: lingering frontline anti-brood parasite defenses in a former host
Authors: Chaumont Matthew H J , Langmore Naomi E , Welbergen Justin A 
Published: February 2021

Abstract
Coevolutionary arms races between brood parasites and hosts provide tractable systems for understanding antagonistic coevolution in nature; however, little is known about the fate of frontline antiparasite defenses when the host “wins” the coevolutionary arms race. By recreating bygone species interactions, using artificial parasitism experiments, lingering defensive behaviors that evolved in the context of parasitism can be understood and may even be used to identify the unknown agent of parasitism past. Here we present the first study of this type by evaluating lingering “frontline” nest defenses that have evolved to prevent egg laying in a former brood parasite host. The Australian reed warbler Acrocephalus australis is currently not parasitized but is known to exhibit fine-tuned egg discrimination—a defensive behavior indicative of a past brood parasite–host arms race and common in closely related parasitized species. Here, using 3D-printed models of adult brood parasites, we examined whether the Australian reed warbler also exhibits frontline defenses to adult brood parasites, and whether we could use these defenses to identify the warbler’s “ghost of parasitism past.” Our findings provide evidence that the Australian reed warbler readily engages in frontline defenses that are considered adaptive specifically in the context of brood parasitism. However, individuals were unable to discriminate between adults of different brood parasite species at their nest. Overall, our results demonstrate that despite a relaxation in selection, defenses against brood parasitism can be maintained across multiple stages of the host’s nesting cycle, and further suggest that, in accordance with previous findings, that learning may be important for fine-tuning frontline defense.
Secretome analysis as a tool to elucidate bacterial contamination influence during second-generation ethanol production in a Melle-Boinot process
Authors: Collograi Karen Cristina , Pereira Isabela de Oliveira , Neitzel Thiago , Martinez-Jimenez Fernan David , da Costa Aline Carvalho , Ienczak Jaciane Lutz 
Published: February 2021

ABSTRACT
Melle-boinot fermentation process can be used to increase the ethanol productivity in second-generation ethanol process (2G). However, bacterial contamination can result in decreased ethanol production and sugars consumption. The available literature on microbial contamination in the 2G at the secretome level, microbial interactions and their impacts on ethanol production are scarce. In this context, the cultivation of Spathaspora passalidarum was studied in pure and co-culture with Lactobacillus fermentum under conditions that mimic the Melle-boinot process. Glucose consumption and ethanol production by S. passalidarum were not affected by bacterial contamination. Xylose consumption was higher in pure culture (11.54 ± 2.62, 16.23 ± 1.76 and 6.50 ± 1.68 g) than in co-culture fermentation (11.89 ± 0.38, 7.29 ± 0.49 and 5.54 ± 2.63 g) in cycle 2. The protein profile of the fermented broth was similar in pure and co-culture fermentation. The low effect of L. fermentum on fermentation and protein profile may be associated with the inhibition of the bacteria by the low nutrient fermentation broth, with centrifugation and/or with sulfuric acid washing. Thereby, considering that research on microbial contamination in the 2G fermentation process is very limited, particularly at the omics level, these findings may contribute to the lignocellulosic biomass fermentation industry.
CFD analysis of jet flows ejected from different nozzles
Authors: Atmaca Mustafa , Çetin Berkay , Ezgi Cüneyt , Kosa Ergin 
Published: February 2021

AbstractNozzles are widely used to control the rate of flow, speed, direction, mass, shape and pressure of the stream in connection with many different engineering applications. This paper presents the performance predicted by a computational fluid dynamic (CFD) model, which are 3D models that utilize parametric analysis, realizable k-epsilon turbulence models and experimental measurement for a jet. Jet flows are ejected from three different slot nozzles: round-shaped nozzle, rectangular-shaped nozzle and 2D-contoured nozzle. In this numerical study, velocities of free jets have been predicted for different axial distances from the nozzle exit in the range of $0.2\le z/B\le 12$ when center velocity at the nozzle exit. CFD simulation results are compared to experimental results from literature. These results are consistent with the existing experiments.
ASAS-NANP SYMPOSIUM: Applications of machine learning for livestock body weight prediction from digital images
Authors: Wang Zhuoyi , Shadpour Saeed , Chan Esther , Rotondo Vanessa , Wood Katharine M , Tulpan Dan 
Published: February 2021

AbstractMonitoring, recording, and predicting livestock body weight (BW) allows for timely intervention in diets and health, greater efficiency in genetic selection, and identification of optimal times to market animals because animals that have already reached the point of slaughter represent a burden for the feedlot. There are currently two main approaches (direct and indirect) to measure the BW in livestock. Direct approaches include partial-weight or full-weight industrial scales placed in designated locations on large farms that measure passively or dynamically the weight of livestock. While these devices are very accurate, their acquisition, intended purpose and operation size, repeated calibration and maintenance costs associated with their placement in high-temperature variability, and corrosive environments are significant and beyond the affordability and sustainability limits of small and medium size farms and even of commercial operators. As a more affordable alternative to direct weighing approaches, indirect approaches have been developed based on observed or inferred relationships between biometric and morphometric measurements of livestock and their BW. Initial indirect approaches involved manual measurements of animals using measuring tapes and tubes and the use of regression equations able to correlate such measurements with BW. While such approaches have good BW prediction accuracies, they are time consuming, require trained and skilled farm laborers, and can be stressful for both animals and handlers especially when repeated daily. With the concomitant advancement of contactless electro-optical sensors (e.g., 2D, 3D, infrared cameras), computer vision (CV) technologies, and artificial intelligence fields such as machine learning (ML) and deep learning (DL), 2D and 3D images have started to be used as biometric and morphometric proxies for BW estimations. This manuscript provides a review of CV-based and ML/DL-based BW prediction methods and discusses their strengths, weaknesses, and industry applicability potential.
Functional diversity vs. monotony: the effect of a multiforage diet as opposed to a single forage diet on animal intake, performance, welfare, and urinary nitrogen excretion
Authors: Garrett Konagh , Beck Matt R , Marshall Cameron J , Fleming Anita E , Logan Chris M , Maxwell Thomas M R , Greer Andrew W , Gregorini Pablo 
Published: February 2021

AbstractThe objective of this study was to determine the effect of offering animals a multiforage choice (MF) of fresh herbages on dry matter intake (DMI), live weight gain, and animal welfare, in comparison with a monotonous diet of ryegrass (Lolium perenne L.). Twenty ram lambs (30.5 ± 0.9 kg initial live weight; mean ± SEM), were randomly allocated to either a diet consisting of diverse MF choice or a single forage ryegrass (SF) diet (n = 10 per treatment) for 35 d. Both diets were fed ad libitum; however, the MF diet was composed of set dry matter ratios of 24% chicory (Cichorium intybus L.), 30% lucerne (Medicago sativa L.), 25% plantain (Plantago lanceolata L.), and 21% ryegrass. The DMI of the MF lambs was 48% greater (P &lt; 0.01) and the within animal day-to-day coefficient of variation (CV) of intake was 26% lower (P &lt; 0.01) than the SF lambs. The average daily gain (ADG) of lambs offered the MF diet was 92% greater (P &lt; 0.01) than the lambs offered the SF diet. The within-animal day-to-day CV of intake was negatively related to ADG (r = −0.59; P &lt; 0.01). The MF lamb’s urinary N concentration was 30% lower (P &lt; 0.01) than that of the SF lambs. The SF lambs spent more time (P &lt; 0.05) exhibiting stereotypic behaviors in the afternoon and spent more time observing other animals than the MF. Overall, allocating an MF choice of fresh herbages as opposed to a single forage diet of ryegrass increases DMI and thereby animal performance, while potentially reducing urinary N excretion.
Effect of Lactic Acid Supplementation on the Growth and Reproduction of Bombyx mori (Lepidopteria: Bombycidae)
Authors: He Zhen , Fang Yang , Li De-Chen , Chen Deng-Song , Wu Fan 
Published: February 2021

Abstract
Lactic acid is widely used in the food, drugs, cosmetics, and other industries to maintain the microbial stability of low-pH products. However, it is unclear whether lactic acid can affect silkworm (Bombyx mori) growth and reproduction. This study investigated the effects of lactic acid on the growth and reproduction of the silkworm. We analyzed the growth, cocoon quality, and reproductive performance of fifth instar larvae fed on mulberry leaves saturated with different concentrations (0.01, 0.1, 1, and 10%) of lactic acid and the control. Results showed that 0.01, 0.1, and 1% lactic acid supplementation positively affects growth and female cocoon quality, with increased larval weight and female cocoon shell weight compared to the control group. In contrast, 10% lactic acid was toxic to the larvae and significantly decreased growth, leading to larval death. Our study provides a basic reference for the optimal amount of preservatives. In addition, this study can be a desirable intervention for sericulturists and can play an important role in getting high return from silkworm-rearing activities.
Metachronous multiple pulmonary nodules 9 years after esophagectomy: a case report
Authors: Hara Kantaro , Matsuda Yumi , Furukawa Nao , Nagano Kohshi 
Published: February 2021

Abstract
A 79-year-old man was referred to our hospital for further examination. He had undergone radical esophagectomy with right thoracotomy 9 years ago. Four cycles of chemotherapy (CDDP +5-FU) were also performed for him. Eight years after esophagectomy, two nodules were identified in the upper lobe of the right lung on chest computed tomography (CT). Owing to the possibility of new primary lung cancer, partial resection was performed. Histopathological examination revealed squamous cell carcinoma. One year and two months later, follow-up chest CT scan revealed a nodule shadow of 1.5 cm in the left apex and a nodule shadow of 0.9 cm below the S9 pleura. Hence, partial left lung resection was performed. Five months after left lung resection, a metastatic liver tumor was found on abdominal CT and left lobectomy of the liver was performed. One year after hepatectomy, the patient died due to peritoneal dissemination.
Dangers that Lurk in a Kiss: Quarantining the American Mouth, 1890–1920
Authors: Baldwin Peter C 
Published: February 2021

Abstract
Affluent women, with the inconsistent support of some medical experts, led an early twentieth-century push to stop the practice of kissing. Imogene Rechtin of Cincinnati and likeminded activists argued that all forms of kissing spread harmful bacteria. The anti-kissing campaign was part of a larger effort to impose stricter discipline over the mouth, which thanks to recent advances in bacteriology had been identified as a dangerous vector of disease. Shaped by the Progressive Era inclination to solve problems through strategies of spatial separation, the effort to “quarantine” the American mouth involved disrupting social practices such as sharing the communion chalice and using a common cup at drinking fountains. The anti-kissing movement also attempted to protect women from unsolicited social kisses from other women and uninvited erotic kisses by men. Though public health officials strongly supported other mouth reforms, they opposed the anti-kissing campaign, largely on the nonmedical grounds that it was an impossible rejection of human sexuality. Then as now, public health arguments over mouth practices have been shaped by deeper battles over individual autonomy and the obligations of the individual to society.
Risk of Nonresponse Bias and the Length of the Field Period in a Mixed-Mode General Population Panel
Authors: Struminskaya Bella , Gummer Tobias 
Published: February 2021

Abstract
Survey researchers are often confronted with the question of how long to set the length of the field period. Longer fielding time might lead to greater participation yet requires survey managers to devote more of their time to data collection efforts. With the aim of facilitating the decision about the length of the field period, we investigated whether a longer fielding time reduces the risk of nonresponse bias to judge whether field periods can be ended earlier without endangering the performance of the survey. By using data from six waves of a probability-based mixed-mode (online and mail) panel of the German population, we analyzed whether the risk of nonresponse bias decreases over the field period by investigating how day-by-day coefficients of variation develop during the field period. We then determined the optimal cut-off points for each mode after which data collection can be terminated without increasing the risk of nonresponse bias and found that the optimal cut-off points differ by mode. Our study complements prior research by shifting the perspective in the investigation of the risk of nonresponse bias to panel data as well as to mixed-mode surveys, in particular. Our proposed method of using coefficients of variation to assess whether the risk of nonresponse bias decreases significantly with each additional day of fieldwork can aid survey practitioners in finding the optimal field period for their mixed-mode surveys.
Travel-associated multidrug-resistant organism acquisition and risk factors among US military personnel
Authors: Buchek Gregory , Mende Katrin , Telu Kalyani , Kaiser Susan , Fraser Jamie , Mitra Indrani , Stam Jason , Lalani Tahaniyat , Tribble David , Yun Heather C 
Published: February 2021

Abstract

Background
International travel is a risk factor for incident colonization with extended spectrum beta-lactamase (ESBL)-producing organisms. These and other multidrug-resistant (MDR) bacteria are major pathogens in combat casualties. We evaluated risk factors for colonization with MDR bacteria in US military personnel travelling internationally for official duty.

Methods
TravMil is a prospective observational study enrolling subjects presenting to military travel clinics. We analysed surveys, antimicrobial use data, and pre- and post-travel perirectal swabs in military travellers to regions outside the continental USA, Canada, Western or Northern Europe, or New Zealand, presenting to one clinic from 12/2015 to 12/2017. Recovered Gram-negative isolates underwent identification and susceptibility testing (BD Phoenix). Characteristics of trip and traveller were analysed to determine risk factors for MDR organism colonization.

Results
110 trips were planned by 99 travellers (74% male, median age 38 years [IQR 31, 47.25]); 72 trips with returned pre- and post-travel swabs were completed by 64 travellers. Median duration was 21 days (IQR 12.75, 79.5). 17% travelled to Mexico/Caribbean/Central America, 15% to Asia, 57% to Africa and 10% to South America; 56% stayed in hotels and 50% in dormitories/barracks. Travellers used doxycycline (15%) for malaria prophylaxis, 11% took an antibiotic for travellers’ diarrhoea (TD) treatment (fluoroquinolone 7%, azithromycin 4%). Incident MDR organism colonization occurred in 8 travellers (incidence density 3.5/1000 travel days; cumulative incidence 11% of trips [95% CI: 4–19%]), all ESBL-producing Escherichia coli. A higher incidence of ESBL-producing E. coli acquisition was associated with travel to Asia (36% vs 7%, P = 0.02) but not with travel to other regions, TD or use of antimicrobials. No relationship was seen between fluoroquinolone or doxycycline exposure and resistance to those antimicrobials.

Conclusions
Incident colonization with MDR organisms occurs at a lower rate in this military population compared with civilian travellers, with no identified modifiable risk factors, with highest incidence of ESBL acquisition observed after South Asia travel.
A spectroscopically confirmed Gaia-selected sample of 318 new young stars within ∼200 pc
Authors: Žerjal Maruša , Rains Adam D , Ireland Michael J , Zhou George , Kammerer Jens , Wallace Alex , Orenstein Brendan J , Nordlander Thomas , Abbot Harrison , Chang Seo-Won 
Published: February 2021

ABSTRACT
In the Gaia era, the majority of stars in the Solar neighbourhood have parallaxes and proper motions precisely determined while spectroscopic age indicators are still missing for a large fraction of low-mass young stars. In this work, we select 756 overluminous late K and early M young star candidates in the southern sky and observe them over 64 nights with the ANU 2.3-m Telescope at Siding Spring Observatory using the Echelle (R = 24 000) and Wide Field spectrographs (WiFeS, R = 3000–7000). Our selection is kinematically unbiased to minimize the preference against low-mass members of stellar associations that dissipate first and to include potential members of diffuse components. We provide measurements of Hα and calcium H&K emission, as well as of Li i 6708 Å in absorption. This enables identification of stars as young as 10–30 Myr – a typical age range for stellar associations. We report on 346 stars showing detectable lithium absorption, 318 of which are not included in existing catalogues of young stars. We also report 125 additional stars in our sample presenting signs of stellar activity indicating youth but with no detectable lithium. Radial velocities are determined for WiFeS spectra with a precision of 3.2 km s−1 and 1.5 km s−1 for the Echelle sample.