bluuebunny/crossref_metadata_2025 huggingface dataset:
Reliability of Anterior Nasal Spine as a Reference Point After LeFort I Surgery Using Three-Dimensional Analysis
Authors: Jung Seoyeon , Kim Jun-Young , Jung Young-Soo , Jung Hwi-Dong
Published: March 2022

To evaluate the stability of maxilla following orthognathic surgery, it is necessary to consider the positional change of various landmarks according to bone remodeling of the maxilla. This study aimed to evaluate the stability of the anterior nasal spine (ANS) as a reliable landmark after orthognathic surgery. Forty-seven patients with skeletal class III malocclusion who underwent bimaxillary orthognathic surgery were included. Skeletal changes were measured using cone-beam computerized tomography at 3 time points: preoperative (T0), 1-month postoperative (T1), and 12-month postoperative (T2). Linear changes of the 6 landmark points of the maxilla were measured in 3 directions: anteroposterior, vertical, and transverse. The data were analyzed with paired t tests, independent t tests, and multiple regression analysis. At 12-month postoperatively, the ANS showed mean (standard deviation) 1.23 (1.07) mm posterior movement (P =
0.00), while other landmarks did not show positional changes, implying bony resorption of ANS. Multiple regression test showed surgical forward movements of ANS (T1-0) affect the postoperative backward changes (β = –0.05, P < 0.05). There was a negative correlation between the surgical movement and postoperative change of ANS by Pearson correlation test (r = –0.38, P < 0.05). The ANS is not a reliable measurement point in three-dimensional superimposition after orthognathic surgery. Therefore, in studying the stability and positional change pattern after LeFort I surgery, it is not recommended to use ANS as a reference point, as changes can occur in the measurement point itself.
A novel animal model of primary blast lung injury and its pathological changes in mice
Authors: Meng Xiang-Yan , Lu Qian-Ying , Zhang Jian-Feng , Li Jun-Feng , Shi Ming-Yu , Huang Si-Yu , Yu Si-Fan , Zhao Yan-Mei , Fan Hao-Jun
Published: March 2022

BACKGROUND

Primary blast lung injury (PBLI) is a major cause of death in military conflict and terrorist attacks on civilian populations. However, the mechanisms of PBLI are not well understood, and a standardized animal model is urgently needed. This study aimed to establish an animal model of PBLI for laboratory study.

METHODS

The animal model of PBLI was established using a self-made mini shock tube simulation device. In brief, mice were randomly divided into two groups: the control group and the model group, the model group were suffered 0.5 bar shock pressures. Mice were sacrificed at 2 hours, 4 hours, 6 hours, 12 hours, and 24 hours after injury. Lung tissue gross observation, hematoxylin and eosin staining and lung pathology scoring were performed to evaluated lung tissue damage. Evans blue dye leakage and bronchoalveolar lavage fluid examination were performed to evaluated pulmonary edema. The relative expression levels of inflammation factors were measured by real-time quantitative polymerase chain reaction and Western blotting analysis. The release of neutrophil extracellular traps was observed by immunofluorescence stain.

RESULTS

In the model group, the gross observation and hematoxylin and eosin staining assay showed the inflammatory cell infiltration, intra-alveolar hemorrhage, and damaged lung tissue structure. The Evans blue dye and bronchoalveolar lavage fluid examination revealed that the lung tissue permeability and edema was significantly increased after injury. Real-time quantitative polymerase chain reaction and Western blotting assays showed that IL-1β, IL-6, TNF-α were upregulated in the model group. Immunofluorescence assay showed that the level of neutrophil extracellular traps in the lung tissue increased significantly in the model group.

CONCLUSION

The self-made mini shock tube simulation device can be used to establish the animal model of PBLI successfully. Pathological changes of PBLI mice were characterized by mechanical damage and inflammatory response in lung tissue.
Label-based expectations affect incentive contrast effects in bumblebees
Authors: Hemingway Claire T. , Muth Felicity
Published: March 2022

While classic models of animal decision-making assume that individuals assess the absolute value of options, decades of research have shown that rewards are often evaluated relative to recent experience, creating incentive contrast effects. Contrast effects are often assumed to be purely sensory, yet consumer and experimental psychology tell us that label-based expectations can affect value perception in humans and rodents. However, this has rarely been tested in non-model systems. Bumblebees forage on a variety of flowers that vary in their signals and rewards and show contrast when rewards are lowered. We manipulated bees' expectations of stimulus quality, before downshifting the reward to induce incentive contrast. We found that contrast effects were not solely driven by experience with a better reward, but also influenced by experience with associated stimuli. While bees' initial response did not differ between treatments, individuals were faster to accept the lower-quality reward when it was paired with a novel stimulus. We explored the boundaries of these label-based expectations by testing bees along a stimulus gradient and found that expectations generalized to similar stimuli. Such reference-dependent evaluations may play an important role in bees' foraging choices, with the potential to impact floral evolution and plant community dynamics.
Large-scale mRNA translation and the intricate effects of competition for the finite pool of ribosomes
Authors: Jain Aditi , Margaliot Michael , Gupta Arvind Kumar
Published: March 2022

We present a new theoretical framework for large-scale mRNA translation using a network of models called the ribosome flow model with Langmuir kinetics (RFMLK), interconnected via a pool of free ribosomes. The input to each RFMLK depends on the pool density, and it affects the initiation rate and potentially also the internal ribosome entry rates along each RFMLK. Ribosomes that detach from an RFMLK owing to termination or premature drop-off are fed back into the pool. We prove that the network always converges to a steady state, and study its sensitivity to variations in the parameters. For example, we show that if the drop-off rate at some site in some RFMLK is increased then the pool density increases and consequently the steady-state production rate in all the
other
RFMLKs increases. Surprisingly, we also show that modifying a parameter of a certain RFMLK can lead to arbitrary effects on the densities along the modified RFMLK, depending on the parameters in the entire network. We conclude that the competition for shared resources generates an indirect and intricate web of mutual effects between the mRNA molecules that must be accounted for in any analysis of translation.
Structural dynamics of real and modelled
Solanum
stamens: implications for pollen ejection by buzzing bees
Authors: Jankauski Mark , Ferguson Riggs , Russell Avery , Buchmann Stephen
Published: March 2022

An estimated 10% of flowering plant species conceal their pollen within tube-like anthers that dehisce through small apical pores (poricidal anthers). Bees extract pollen from poricidal anthers through a complex motor routine called floral buzzing, whereby the bee applies vibratory forces to the flower stamen by rapidly contracting its flight muscles. The resulting deformation depends on the stamen's natural frequencies and vibration mode shapes, yet for most poricidal species, these properties have not been sufficiently characterized. We performed experimental modal analysis on
Solanum elaeagnifolium
stamens to quantify their natural frequencies and vibration modes. Based on morphometric and dynamic measurements, we developed a finite-element model of the stamen to identify how variable material properties, geometry and bee weight could affect its dynamics. In general, stamen natural frequencies fell outside the reported floral buzzing range, and variations in stamen geometry and material properties were unlikely to bring natural frequencies within this range. However, inclusion of bee mass reduced natural frequencies to within the floral buzzing frequency range and gave rise to an axial-bending vibration mode. We hypothesize that floral buzzing bees exploit the large vibration amplification factor of this mode to increase anther deformation, which may facilitate pollen ejection.
The use of zeolite-based geopolymers as adsorbent for copper removal from aqueous media
Authors: Baykara Haci , Mendoza Solorzano Maria de Lourdes , Delgado Echeverria Jose Javier , Cornejo Mauricio H. , Tapia-Bastidas Clotario V.
Published: March 2022

Copper has been proven to have hazardous effects on human beings depending on its concentration levels. Recently, there has been a growing interest in developing geopolymers using local industrial minerals and by-products. However, research on the adsorption of heavy metals by geopolymer based on mordenite-rich tuffs is still limited. The geopolymer adsorbents have been synthesized using natural Ecuadorian zeolite-rich tuffs containing quartz, mordenite calcite and amorphous content with 20.8%, 28.5%, 4.2% and 46.4%, respectively. The geopolymers showed a maximum compressive strength of 26.86 MPa for 28 d of curing time. In the present study, an Ecuadorian zeolite-based geopolymer's removal capacity on copper ions in aqueous solutions, varying concentration and contact time were tested. Kinetic models were developed using pseudo first-order, pseudo second-order and the Elovich model. The adsorption data, using Cu
2+
concentrations from 20 to 160 ppm, at 25°C were described by the Langmuir and Freundlich isotherms. Linear coefficient of determination (
R
2
) results show that the Langmuir model fits the best. The attained adsorption capacity of 52.63 mg g
−1
demonstrates the low-cost geopolymer's effectiveness for this study and its competitiveness compared with other studies. Adsorption kinetics follows the pseudo second-order kinetics model at the lower initial concentration of Cu
2+
.
Asymptotic analysis of subglacial plumes in stratified environments
Authors: Bradley Alexander T. , Rosie Williams C. , Jenkins Adrian , Arthern Robert
Published: March 2022

Accurate predictions of basal melt rates on ice shelves are necessary for precise projections of the future behaviour of ice sheets. The computational expense associated with completely resolving the cavity circulation using an ocean model makes this approach unfeasible for multi-century simulations, and parametrizations of melt rates are required. At present, some of the most advanced melt rate parametrizations are based on a one-dimensional approximation to the melt rate that emerges from the theory of subglacial plumes applied to ice shelves with constant basal slopes and uniform ambient ocean conditions; in this work, we present an asymptotic analysis of the corresponding equations in which non-constant basal slopes and typical ambient conditions are imposed. This analysis exploits the small aspect ratio of ice shelf bases, the relatively weak thermal driving and the relative slenderness of the region separating warm, salty water at depth and cold, fresh water at the surface in the ambient ocean. We construct an approximation to the melt rate that is based on this analysis, which shows good agreement with numerical solutions in a wide variety of cases, suggesting a path towards improved predictions of basal melt rates in ice-sheet models.
Coupling-induced instability in a ring of thermoacoustic oscillators
Authors: Pedergnana T. , Noiray N.
Published: March 2022

Thermoacoustic instabilities in can-annular combus-tors of stationary gas turbines lead to unstable Bloch modes which appear as rotating acoustic pressure waves along the turbine annulus. The multiscale, multiphysical nature of the full problem makes a detailed analysis challenging. In this work, we derive a low-order, coupled oscillators model of an idealized can-annular combustor. The unimodal projection of the Helmholtz equation for the can acoustics is combined with the Rayleigh conductivity, which describes the aeroacoustic coupling between neighbouring cans. Using a Bloch-wave ansatz, the resulting system is reduced to a single equation for the frequency spectrum. A linear stability analysis is then performed to study the perturbation of the spectrum by the can-to-can interaction. It is observed that the acoustic coupling can suppress or amplify thermoacoustic instabilities, raising the potential for instabilities in nominally stable systems.
Climate change and lithium mining influence flamingo abundance in the Lithium Triangle
Authors: Gutiérrez Jorge S. , Moore Johnnie N. , Donnelly J. Patrick , Dorador Cristina , Navedo Juan G. , Senner Nathan R.
Published: March 2022

The development of technologies to slow climate change has been identified as a global imperative. Nonetheless, such ‘green’ technologies can potentially have negative impacts on biodiversity. We explored how climate change and the mining of lithium for green technologies influence surface water availability, primary productivity and the abundance of three threatened and economically important flamingo species in the ‘Lithium Triangle’ of the Chilean Andes. We combined climate and primary productivity data with remotely sensed measures of surface water levels and a 30-year dataset on flamingo abundance using structural equation modelling. We found that, regionally, flamingo abundance fluctuated dramatically from year-to-year in response to variation in surface water levels and primary productivity but did not exhibit any temporal trends. Locally, in the Salar de Atacama—where lithium mining is focused—we found that mining was negatively correlated with the abundance of two of the three flamingo species. These results suggest continued increases in lithium mining and declines in surface water could soon have dramatic effects on flamingo abundance across their range. Efforts to slow the expansion of mining and the impacts of climate change are, therefore, urgently needed to benefit local biodiversity and the local human economy that depends on it.
Determinants of Neonatal Sepsis Admitted In Neonatal Intensive Care Unit At Public Hospitals Of Kaffa Zone, South West Ethiopia
Authors: Belayneh Melesse , Getaneh Gebremariam , Gebretsadik Alemaw
Published: March 2022

Background

Neonatal sepsis is a systemic inflammatory response syndrome in the presence of infection during the first 28 days of life. Globally every year about 4 million children die in the first 4 weeks of life, of which 99% of the deaths occur in low and middle income countries and the most common causes of neonatal death in Ethiopia. Identification of the determinants for neonatal sepsis and treatment of newborns with sepsis is not adequate in low income countries like Ethiopia especially in southern part of the country.

Objective

To identify determinants of neonatal sepsis admitted in neonatal intensive care unit at public hospitals of Kaffa zone, south west Ethiopia 2021.

Methods

Institutional based unmatched case control study was conducted on a total sample of 248 (62 cases and 186 controls) in public Hospitals of kaffa zone from March to April 2021.The collected data were entered, coded and cleaned by Epidata version 3.1 and it was exported to SPSS version 25. Bi-variable and multivariable logistic regression was conducted. Variables with (p< 0.25) in bi-variable logistic regression analysis, were entered to multivariable logistic regression and then determinants which is statistical significant will be declared at P<0.05.

Result

A total of 248 (62 cases and 186 controls) were included in the study. variables like prolonged rupture of membrane ≥18 hours [AOR =5.13, 95%CI=1.38-19.05], meconium stained amniotic fluid[AOR =6.03, 95%CI=2.16-16.90], intra-partum fever [AOR =8.26, 95%CI=3.12-21.97], urinary tract infections [AOR=14,55, 95%CI=4.91-43.10], breast feeding after a hour [AOR =3.9, 95%CI=1.27-12.02], resuscitation [AOR =13.25, 95%CI=3.44-51.01], no chlorohexidine application [AOR =4.27, 95%CI=1.65-11.08] were significantly associated with neonatal sepsis.

Conclusion and Recommendation

Among the variables prolonged rupture of membranes, meconium stained amniotic fluid, intra-partum fever, UTI/STI, and not breast feeding with in a hour were maternal variables and resuscitation at birth and not application of chlorohexidine ointment on the umbilicus were neonatal variables that were found to be neonatal-related risk factors of neonatal sepsis. Infection prevention strategies and clinical management need to be strengthening and/or implementing by providing especial attention for the specified determinants.
VinDr-PCXR: An open, large-scale chest radiograph dataset for interpretation of common thoracic diseases in children
Authors: Nguyen Ngoc H. , Pham Hieu H. , Tran Thanh T. , Nguyen Tuan N.M. , Nguyen Ha Q.
Published: March 2022

Computer-aided diagnosis systems in adult chest radiography (CXR) have recently achieved great success thanks to the availability of large-scale, annotated datasets and the advent of high-performance supervised learning algorithms. However, the development of diagnostic models for detecting and diagnosing pediatric diseases in CXR scans is undertaken due to the lack of high-quality physician-annotated datasets. To overcome this challenge, we introduce and release VinDr-PCXR, a new pediatric CXR dataset of 9,125 studies retrospectively collected from a major pediatric hospital in Vietnam between 2020 and 2021. Each scan was manually annotated by a pediatric radiologist who has more than ten years of experience. The dataset was labeled for the presence of 36 critical findings and 15 diseases. In particular, each abnormal finding was identified via a rectangle bounding box on the image. To the best of our knowledge, this is the first and largest pediatric CXR dataset containing lesion-level annotations and image-level labels for the detection of multiple findings and diseases. For algorithm development, the dataset was divided into a training set of 7,728 and a test set of 1,397. To encourage new advances in pediatric CXR interpretation using data-driven approaches, we provide a detailed description of the VinDr-PCXR data sample and make the dataset publicly available on https://physionet.org/.
Risk of myocarditis and pericarditis following BNT162b2 and ChAdOx1 COVID-19 vaccinations
Authors: Ip Samantha , Torabi Fatemeh , Denaxas Spiros , Akbari Ashley , Abbasizanjani Hoda , Knight Rochelle , Cooper Jennifer , Denholm Rachel , Keene Spencer , Bolton Thomas , Hollings Sam , Omigie Efosa , North Teri-Louise , Suseeladevi Arun Karthikeyan , Angelantonio Emanuele Di , Khunti Kamlesh , Sterne Jonathan A C , Sudlow Cathie , Whiteley William , Wood Angela , Walker Venexia
Published: March 2022

We describe our analyses of data from over 49.7 million people in England, representing near-complete coverage of the relevant population, to assess the risk of myocarditis and pericarditis following BNT162b2 and ChAdOx1 COVID-19 vaccination. A self-controlled case series (SCCS) design has previously reported increased risk of myocarditis after first ChAdOx1, BNT162b2, and mRNA-1273 dose and after second doses of mRNA COVID-19 vaccines in England. Here, we use a cohort design to estimate hazard ratios for hospitalised or fatal myocarditis/pericarditis after first and second doses of BNT162b2 and ChAdOx1 vaccinations. SCCS and cohort designs are subject to different assumptions and biases and therefore provide the opportunity for triangulation of evidence. In contrast to the findings from the SCCS approach previously reported for England, we found evidence for lower incidence of hospitalised or fatal myocarditis/pericarditis after first ChAdOx1 and BNT162b2 vaccination, as well as little evidence to suggest higher incidence of these events after second dose of either vaccination.
The Relationship between Continuity of Care with a Primary Care Provider and Duration of Work Disability in Workers with Low Back Pain: A Retrospective Cohort Study
Authors: Sheehan Luke R , Di Donato Michael , Gray Shannon E , Lane Tyler J , van Vreden Caryn , Collie Alex
Published: March 2022

Objective

To determine the continuity of care (CoC) provided by general practitioners among workers with low back pain; identify personal, workplace and social factors associated with CoC in this population; and investigate if CoC is associated with working time loss.

Data sources

An administrative database containing accepted workers’ compensation claim and service level data, for workers with back pain from five Australian jurisdictions, injured between July 2010 and June 2015.

Study Design

A retrospective cohort study. Outcomes were CoC with a general practitioner, measured with the Usual Provider Continuity index, and working time loss, measured as the number of weeks for which workers’ compensation income support benefits were paid.

Extraction methods

Eligible workers had at least four general practitioner services, and greater than two weeks working time loss. Usual Provider Continuity index score was categorised as complete, high, moderate, or low CoC. Ordinal logistic regression models examined factors associated with Usual Provider Continuity category. Quantile regression models examined association between duration of working time loss and Usual Provider Continuity category, in four groups with different volumes of general practitioner services.

Principal Findings

Complete CoC was observed in 33.8% of workers, high CoC among 37.7%, moderate CoC in 22.1%, and low CoC in 6.4%. Higher Usual Provider Continuity was associated with fewer general practitioner services, older age, living in urban areas, an occupation as a Community and Personal Service Worker or Clerical and Administrative Worker, and the state of Victoria. In workers with more than two months of time loss, those with complete CoC consistently had shorter durations of time loss.

Conclusions

Higher CoC with a general practitioner is associated with less working time loss and this relationship is strongest in the sub-acute phase of low back pain.

Callout Box

What is known on this topic

Continuity of care is a key component of best practice primary care

Low back pain is a condition that often requires ongoing management and care from a general practitioner

The relationship between continuity of care and work disability duration, recovery and return to work in workers with low back pain is not known

What this study adds

Workers with low back pain who see the same general practitioner for all services (i.e., have a greater continuity of care) generally have shorter durations of working time loss

Higher continuity of care was observed in workers who had fewer PCP services, were aged over 45, lived in urban areas, and worked as a Community and Personal Service Worker or Clerical and Administrative Worker

Workers’ compensation systems should consider policies and guidelines that increase continuity of care in injured workers
Acute temporal effect of ambient air pollution on common congenital cardiovascular defects and cleft palate: a case-crossover study
Authors: Enebish Temuulen , Franklin Meredith , Habre Rima , Breton Carrie , Tuvshindorj Nomindelger , Tumur Gantuya , Munkhuu Bayalag , Warburton David
Published: March 2022

This symmetric bidirectional case-crossover study examined the association between short-term ambient air pollution exposure during weeks 3-8 of pregnancy and certain common congenital anomalies in Ulaanbaatar, Mongolia, between 2014 and 2018. Using predictions from a Random Forest regression model, authors assigned daily ambient air pollution exposure of particulate matter <2.5 um aerodynamic diameter, sulphur dioxide, nitrogen dioxide, and carbon monoxide for each subject based on their administrative area of residence. We used conditional logistic regression with adjustment for corresponding apparent temperature to estimate relative odds of select congenital anomalies per IQR increase in mean concentrations and quartiles of air pollutants. The adjusted relative odds of cardiovascular defects (ICD-10 subchapter: Q20-Q28) was 2.64 (95% confidence interval: 1.02-6.87) per interquartile range increase in mean concentrations of particulate matter <2.5 um aerodynamic diameter for gestational week 7. This association was further strengthened for cardiac septal defects (ICD-10 code: Q21, odds ratio: 7.28, 95% confidence interval: 1.6-33.09) and isolated ventricular septal defects (ICD-10 code: Q21.0, odds ratio: 9.87, 95% confidence interval: 1.6-60.93). We also observed an increasing dose-response trend when comparing the lowest quartile of air pollution exposure with higher quartiles on weeks 6 and 7 for Q20-Q28 and Q21 and week 4 for Q21.0. Other notable associations include increased relative odds of cleft lip and cleft palate subchapter (Q35-Q37) and PM2.5 (OR: 2.25, 95% CI: 0.62-8.1), SO2 (OR: 2.6, 95% CI: 0.61-11.12), and CO (OR: 2.83, 95% CI: 0.92-8.72) in week 4. Our findings contribute to the limited body of evidence regarding the acute effect of ambient air pollution exposure on common adverse birth outcomes.
Organ- and function-specific anatomical organization of the vagus nerve supports fascicular vagus nerve stimulation
Authors: Jayaprakash Naveen , Song Weiguo , Toth Viktor , Vardhan Avantika , Levy Todd , Tomaio Jacquelyn , Qanud Khaled , Mughrabi Ibrahim , Chang Yao-Chuan , Rob Moontahinaz , Daytz Anna , Abbas Adam , Nassrallah Zeinab , Volpe Bruce T. , Tracey Kevin J. , Al-Abed Yousef , Datta-Chaudhuri Timir , Miller Larry , Barbe Mary F. , Lee Sunhee C. , Zanos Theodoros P. , Zanos Stavros
Published: March 2022

Vagal fibers travel inside fascicles and form branches to innervate organs and regulate organ functions. Vagus nerve stimulation (VNS) therapies activate fibers non-selectively, often resulting in reduced efficacy and side effects from non-targeted organs. Transverse and longitudinal arrangement of fibers according to functions they mediate and organs they innervate is unknown, however it is crucial for selective VNS. Using microcomputed tomography, we found that, in swine, fascicles are arranged in 2 overlapping axes, with sensory and motor fascicles separated cephalad and merging caudad, and larynx-, heart- and lung-specific fascicles separated caudad and progressively merging cephalad. Using immunohistochemistry, we found that the distribution of single fibers is highly nonuniform: myelinated afferents and efferents occupy separate fascicles, unmyelinated efferents co-localize with myelinated afferents, and small unmyelinated afferents are widely distributed. Using a multi-contact cuff electrode, we delivered fascicular cervical VNS in anesthetized and awake swine. Compound action potentials, from distinct fiber types, and organ responses, including laryngeal muscle, cough, breathing, heart rate and blood pressure responses are elicited in a radially asymmetric manner, with consistent angular separations. These results indicate that vagal fibers are anatomically organized according to functions they mediate and organs they innervate and can be asymmetrically activated by fascicular cervical VNS.
Predicting plant-related and leaf-related parameters of winter wheat using vegetation index: Should phenological correction be applied across growth stages?
Authors: Zhao Yu , Meng Yang , Feng Haikuan , Han Shaoyu , Yang Guijun , Li Zhenhai
Published: March 2022

Most existing plant-related and leaf-related parameters models of winter wheat vary across growing seasons, but it is an open question whether a unified statistical model can be developed to predict plant-related and leaf-related parameters using VI across multiple growing seasons, or whether the phenological correction is necessary for each parameter across multiple growing seasons. To explore this question, we measured two plant-related parameters and four leaf-related parameters over five growth stages during the 2017–2021 growing seasons. A hierarchical linear model (HLM) automatically adapts the relationship between VIs and their corresponding parameter across growing seasons and assesses the contribution of phenological variables by applying a sensitivity analysis. The estimates of VI–plant-related parameters [aboveground dry biomass (AGB) and plant nitrogen concentration (PNC)] were scattered over a given growing season, unlike the relationship between VI–leaf-related parameters [leaf dry biomass (LGB), leaf nitrogen concentration (LNC), leaf area index (LAI) and soil and plant analysis development (SPAD)]. In contrast, the AGB, PNC, LGB, LNC, LAI, and SPAD HLM models are stable and can be popularized across growing seasons, with the determination coefficient R2 ranging from 0.84 to 0.86, 0.79 to 0.87, 0.70 to 0.71, 0.68 to 0.86, 0.75 to 0.81, and 0.68 to 0.70, respectively, and the root mean square error ranging from 0.13 to 0.50 t/ha, 0.01 to 0.07%, 0.01 to 0.03 t/ha, 0.02 to 0.03%, 0.02 to 0.07, and 0.47 to 0.69, respectively. The sensitivity index of the phenological information in the AGB and PNC models was 0.56–0.78 and 0.66–0.72, respectively, whereas that in the LGB, LNC, LAI, and SPAD models was 0.01–0.06, 0.01–0.10, 0.02–0.06, and 0.00–0.01, respectively. Although phenological effects have little effect on leaf-related indicators, HLM has a strong potential for application to other crops and regions.
An optimal variant to gene distance window derived from an empirical definition of cis and trans protein QTLs
Authors: Fauman Eric B , Hyde Craig
Published: March 2022

Background

A genome-wide association study (GWAS) correlates variation in the genotype with variation in the phenotype across a cohort, but the causal gene mediating that impact is often unclear. When the phenotype is protein abundance, a reasonable hypothesis is that the gene encoding that protein is the causal gene. However, as variants impacting protein levels can occur thousands or even millions of base pairs from the gene encoding the protein, it is unclear at what distance this simple hypothesis breaks down.

Results

By making the simple assumption that cis-pQTLs should be distance dependent while trans-pQTLs are distance independent, we arrive at a simple and empirical distance cutoff separating cis- and trans-pQTLs. Analyzing a recent large-scale pQTL study (Pietzner, 2021) we arrive at an estimated distance cutoff of 944 kilobasepairs (kbp) (95% confidence interval: 767–1,161) separating the cis and trans regimes.

Conclusions

We demonstrate that this simple model can be applied to other molecular GWAS traits. Since much of biology is built on molecular traits like protein, transcript and metabolite abundance, we posit that the mathematical models for cis and trans distance distributions derived here will also apply to more complex phenotypes and traits.
Learning to Control Complex Rehabilitation Robot Using High-Dimensional Interfaces
Authors: Lee Jongmin M. , Gebrekristos Temesgen , De Santis Dalia , Nejati-Javaremi Mahdieh , Gopinath Deepak , Parikh Biraj , Mussa-Ivaldi Ferdinando A. , Argall Brenna D.
Published: March 2022

Upper body function is lost when injuries are sustained to the cervical spinal cord. Assistive machines can support the loss in upper body motor function. To regain functionality at the level of performing activities of daily living (e.g., self-feeding), though, assistive machines need to be able to operate in high dimensions. This means there is a need for interfaces with the capability to match high-dimensional operation. The body-machine interface provides this capability and has shown to be a suitable interface even for individuals with limited mobility. This is because it can take advantage of people’s available residual body movements. Previous studies using this interface have only shown that the interface can control low-dimensional assistive machines. In this pilot study, we demonstrate the interface can scale to high-dimensional robots, can be learned to control a 7-dimensional assistive robotic arm, to perform complex reaching and functional tasks, by an uninjured population. We also share results from various analyses that hint at learning, even when performance is extremely low. Decoupling intrinsic correlations between robot control dimensions seem to be a factor in learning—that is, proficiency in activating each control dimension independently may contribute to learning and skill acquisition of high-dimensional robot control. In addition, we show that learning to control the robot and learning to perform complex movement tasks can occur simultaneously.
Sizing up spotted lanternfly nymphs for instar determination and growth allometry
Authors: Bien Theodore , Alexander Benjamin H. , White Eva , Hsieh S. Tonia , Kane Suzanne Amador
Published: March 2022

A major ongoing research effort seeks to understand the behavior, ecology and control of the spotted lanternfly (SLF) (Lycorma delicatula), a highly invasive pest in the U.S. and South Korea. These insects undergo four nymphal stages (instars) before reaching adulthood, and appear to shift host plant preferences, feeding, dispersal and survival patterns, anti-predator behaviors, and response to traps and chemical controls with each stage. However, categorizing SLF life stage is challenging for the first three instars, which have the same coloration and shape, because no comprehensive datasets exist. We present a dataset of body mass and length for SLF nymphs throughout two growing seasons and compare our results with previously-published ranges of instar body lengths. An analysis using two clustering methods revealed that 1st-3rdinstar body mass and length fell into distinct clusters that were consistent between years, supporting using these metrics to stage nymphs during a single growing season. However, the ranges for 2nd-4th instars were not consistent between our results and those from earlier studies for diverse locations. The scaling of SLF nymph body mass with body length varied between isometry (constant shape) and positive allometry (growing faster than predicted by isometry) in the two years studied. Using previously published data, we also found that SLF nymph adhesive footpad area varies in direct proportion to weight, suggesting that footpad adhesion is independent of nymphal stage, while their tarsal claws display positive allometry and hence disproportionately increasing grasp (mechanical adhesion). By contrast, mouthpart dimensions are weakly correlated with body length, consistent with predictions that these features should reflect preferred host plant characteristics rather than body size. We recommend future studies use the body mass vs length growth curve as a fitness benchmark to study how SLF instar development depends on factors such as hatch date, host plant, temperature, and geographic location, to further understanding of life history patterns that help prevent further spread of this invasive insect.
Insertion ofYFPatP5CS1andAFL1shows the potential, and potential complications, of gene tagging for functional analyses of stress-related proteins
Authors: Longkumer Toshisangba , Grillet Louis , Chang Hao-Yi , Lường Tài Chiến , Chen Chih-Yun , Putra Hadi , Schmidt Wolfgang , Verslues Paul E.
Published: March 2022

Crispr/CAS9-enabled homologous recombination to insert a tag in frame with an endogenous gene can circumvent difficulties such as context-dependent promoter activity that complicate analysis of gene expression and protein accumulation patterns. However, there have been few reports examining whether such Gene Targeting/Gene Tagging (GT) can alter expression of the target gene. The enzyme encoded by Δ1-pyrroline-5-carboxylate synthetase 1(P5CS1) is key for stress-induced proline synthesis and drought resistance, yet its expression pattern and protein localization have been difficult to assay. We used GT to insertYFPin frame with the 5’ or 3’ ends of the endogenousP5CS1andAt14a-Like 1(AFL1) coding regions. Insertion at the 3’ end of either gene generated homozygous lines with expression of thegene-YFPfusion indistinguishable from the wild type allele. However, forP5CS1this occurred only after selfing and advancement to the T5generation allowed initial homozygous lethality of the insertion to be overcome. Once this was done, the GT-generated P5CS1-YFP plants revealed new information about P5CS1 localization and tissue-specific expression. In contrast, insertion ofYFPat the 5’ end of either gene blocked expression. The results demonstrate that GT can be useful for functional analyses of genes that are problematic to properly express by other means but also show that, in some cases, GT can disrupt expression of the target gene.

Summary statement

Gene tagging ofArabidopsis thaliana P5CS1andAFL1shows the potential of GT for functional analysis of stress-related genes, but also provides examples of how GT can dramatically disrupt expression of the target gene.
Bayesian multi-model-based 13C15N-metabolic flux analysis quantifies carbon-nitrogen metabolism in mycobacteria
Authors: Borah Khushboo , Beyß Martin , Xu Ye , Barber Jim , Costa Catia , Newcombe Jane , Theorell Axel , Bailey Melanie J , Beste Dany JV , McFadden Johnjoe , Nöh Katharina
Published: March 2022

Metabolic flux is the final output of cellular regulation and has been extensively studied for carbon but much less is known about nitrogen, which is another important building block for living organisms. For the pathogen Mycobacterium tuberculosis (Mtb), this is particularly important in informing the development of effective drugs targeting Mtb’s metabolism. Here we performed 13C15N dual isotopic labelling of mycobacterial steady state cultures and quantified intracellular carbon-nitrogen (CN) and nitrogen (N) fluxes in addition to carbon (C) fluxes and inferred their reaction bidirectionalities. The combination of 13C15N-MFA with a Bayesian multi-model approach allowed us to resolve C and N fluxes simultaneously which was not possible with classical 13C-MFA. We quantified CN fluxes for amino acid and, for the first time, nucleotide biosynthesis. Our analysis identified glutamate as the central CN and N node in mycobacteria, and improved resolution of the anaplerotic node. Our study describes a powerful platform to measure carbon and nitrogen metabolism in any biological system with statistical rigor.
A CRISPR screen identifies redox vulnerabilities for KEAP1/NRF2 mutant non-small cell lung cancer
Authors: Jiang Chang , Ward Nathan P. , Prieto-Farigua Nicolas , Kang Yun Pyo , Thalakola Anish , Teng Mingxiang , DeNicola Gina M.
Published: March 2022

The redox regulator NRF2 is hyperactivated in a large percentage of non-small cell lung cancer (NSCLC) cases, which is associated with chemotherapy and radiation resistance. To identify redox vulnerabilities for KEAP1/NRF2 mutant NSCLC, we conducted a CRISPR-Cas9-based negative selection screen for antioxidant enzyme genes whose loss sensitized cells to sub-lethal concentrations of the superoxide (O2•−)-generating drug β-Lapachone. While our screen identified expected hits in the pentose phosphate pathway, the thioredoxin-dependent antioxidant system, and glutathione reductase, we also identified the mitochondrial superoxide dismutase 2 (SOD2) as one of the top hits. Surprisingly, β-Lapachone did not generate mitochondrial O2•−but rather SOD2 loss enhanced the efficacy of β-Lapachone due to loss of iron-sulfur protein function, loss of mitochondrial ATP maintenance and deficient NADPH production. Importantly, inhibition of mitochondrial electron transport activity sensitized to β-Lapachone, demonstrating these effects may be translated to increase ROS sensitivity therapeutically.
A Non-conventional Archaeal Fluorinase Identified by In Silico Mining Catalyzes the Fastest Natural Nucleophilic Fluorination
Authors: Pardo Isabel , Bednar David , Calero Patricia , Volke Daniel C. , Damborský Jiří , Nikel Pablo I.
Published: March 2022

Fluorinases, the only enzymes known to catalyze the transfer of fluorine to an organic molecule, are essential biocatalysts for the sustainable synthesis of valuable organofluorines. However, the few fluorinases identified so far have low turnover rates that hamper biotechnological applications. Here, we isolated and characterized putative fluorinases retrieved from systematic in silico mining and identified a non-conventional archaeal enzyme from Methanosaeta sp. that mediates the highest fluorination rate reported to date. Furthermore, we demonstrate enhanced production of fluoronucleotides in vivo in a bacterial host engineered with this archaeal fluorinase, paving the way towards synthetic metabolism for efficient biohalogenations.

Fastest biological SN2 fluorination
Inter- and intra-Subunit interactions driving the MukBEF ATPase
Authors: Bahng Soon , Kumar Rupesh , Marians Kenneth J.
Published: March 2022

MukBEF, an SMC-like protein complex, is the bacterial condensin. It is likely that it compacts DNA via an ATP hydrolysis-dependent, DNA loop-extrusion reaction as has been demonstrated for the yeast SMC proteins condensin and cohesin. MukB also interacts with the ParC subunit of the cellular chromosomal decatenase topoisomerase IV, an interaction that is required for proper chromosome condensation and segregation in E. coli, although it suppresses the MukB ATPase activity. We have investigated the MukBEF ATPase activity, identifying inter- and intra-subunit interactions by protein-protein crosslinking and site-specific mutagenesis. We show that interactions between the hinge of MukB and its neck region are essential for the ATPase activity, that the ParC subunit of Topo IV inhibits the MukB ATPase by preventing this interaction, that MukE interaction with DNA is likely essential for viability, and that interactions between MukF and the MukB neck region are necessary for ATPase activity and viability.
PtdIns(3,4)P2, Lamellipodin, and VASP coordinate cytoskeletal remodeling during phagocytic cup formation in macrophages
Authors: Montaño-Rendón Fernando , Walpole Glenn F. W. , Krause Matthias , Hammond Gerald R.V. , Grinstein Sergio , Fairn Gregory D.
Published: March 2022

Phosphoinositides are pivotal regulators of vesicular traffic and signaling during phagocytosis. Phagosome formation, the initial step of the process, is characterized by local membrane remodelling and reorganization of the actin cytoskeleton that leads to formation of the pseudopods that drive particle engulfment. Using genetically-encoded fluorescent probes we found that upon particle engagement a localized pool of PtdIns(3,4)P2 is generated by the sequential activities of class I phosphoinositide 3-kinases and phosphoinositide 5-phosphatases. Depletion of the enzymes responsible for this locally generated pool of PtdIns(3,4)P2 blocks pseudopod progression and ultimately phagocytosis. We show that the PtdIns(3,4)P2 effector Lamellipodin (Lpd) is recruited to nascent phagosomes by PtdIns(3,4)P2. Furthermore, we show that silencing of Lpd inhibits phagocytosis and produces aberrant pseudopodia with disorganized actin filaments. Lastly, vasodilator-stimulated phosphoprotein (VASP) was identified as a key actin-regulatory protein mediating phagosome formation downstream of Lpd. Mechanistically, our findings imply that a pathway involving PtdIns(3,4)P2, Lpd and VASP mediates phagocytosis at the stage of particle engulfment.
Social closeness modulates brain dynamics during distrust anticipation
Authors: Jiménez Said , Mercadillo-Caballero Roberto , Angeles-Valdes Diego , Sánchez-Sosa Juan José , Muñoz-Delgado Jairo , Garza-Villarreal Eduardo A.
Published: March 2022

Anticipation of trust from a partner with high social closeness generates the preconditions for cooperative and reciprocal interactions to occur. However, if there is uncertainty in the interaction because the partner is a stranger or because the person has mistrusted us on another occasion, an aversive experience is generated. Hence, low social closeness or mistrust makes people keep track of the other’s behavior. In case of experiencing deviations from social norms, the person will monitor the intentions of the partner and update their priors regarding their social preferences. The anterior insula (AIns) seems to be sensitive to these social norm violations in functional magnetic resonance imaging (fMRI) experiments, however, the monitoring of partners with different levels of social closeness has not been investigated. In our study we wanted to find the brain regions related to (dis)trust anticipation from partners who differ in their level of social closeness. For this, we designed an experiment in which participants played an economic decision game with three people (trustors): A computer, a stranger, and a real friend. We covertly manipulated their decisions in the game so that they unexpectedly distrusted our participants. Using task-fMRI, our whole-brain analysis found that the AIns was active during the anticipation of the decisions from human partners (humans vs computer), but not during anticipation between high and low social closeness (friend vs stranger). However, using a psychophysiological interaction analysis, we found increases in functional coupling between the AIns and regions in the “mentalizing” network (such as temporal regions and parieto-occipital cortices) during trust anticipation between a high versus low social closeness partner. These results suggest that there may be a modulation of the AIns activity, specifically for high social closeness trustors, by regions that encode the intentions underlying the truster behavior.
Measuring the efficiency of Indian public and private banks using the two-stage network DEA model
Authors: Kumar Vijyapu Prasanna , Kar Sujata
Published: March 2022

Purpose

The main objective of this paper is to present a holistic approach for measuring overall bank efficiency and its decomposition in intermediation and profitability efficiencies.

Design/methodology/approach

Two-stage network data envelopment analysis (NDEA) model has been used for obtaining intermediation and profitability efficiencies along with overall bank efficiency. Additionally, bootstrap truncated regression has also been adopted to explore the influential predictors of two stages.

Findings

A comparative analysis between Indian private-sector and public-sector banks showed that the former is efficient than the latter in profitability efficiency stage. Another interesting finding is that none of the banks is efficient in overall study tenure. Finally, outcomes of bootstrap truncated regression show that differences in intermediation efficiency are explained by firm size, return on asset, market share and ownership while profitability stage is determined by diverse, gross domestic product and ownership.

Research limitations/implications

This study will guide the Indian banking sector to act on which they are lagging, for the betterment of their overall performances. Finally, parameters like loan waives and disposal income of non-performing assets (NPAs) are not considered because of the unavailability of information in the output measures of NDEA model.

Originality/value

This paper not only provides a detailed performance assessment of Indian banks but also examines banks’ internal efficiency by deposits as an intermediary measure.