bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of Coronavirus Disease 2019 (Covid-19), a Nationwide Mass Casualty Disaster on Intensive Care Units: Clinical Outcomes and Associated Cost-of-Care
Authors: Henning Allison M. , Thomas Neal J. , Williams Duane C. , Shore David M. , Memmi Michelle E. , Wang Li
Published: June 2022

Objective:

The COVID-19 pandemic resulted in millions of deaths worldwide and is considered a significant mass-casualty disaster (MCD). The surge of patients and scarcity of resources negatively impacted hospitals, patients and medical practice. We hypothesized ICUs during this MCD had a higher acuity of illness, and subsequently had increased lengths of stay (LOS), complication rates, death rates and costs of care. The purpose of this study was to investigate those outcomes.

Methods:

This was a multicenter, retrospective study that compared intensive care admissions in 2020 to those in 2019 to evaluate patient outcomes and cost of care. Data were obtained from the Vizient Clinical Data Base/Resource Manager (Vizient Inc., Irvine, Texas, USA).

Results:

Data included the number of ICU admissions, patient outcomes, case mix index and summary of cost reports. Quality outcomes were also collected, and a total of 1304981 patients from 333 hospitals were included. For all medical centers, there was a significant increase in LOS index, ICU LOS, complication rate, case mix index, total cost, and direct cost index.

Conclusion:

The MCD caused by COVID-19 was associated with increased adverse outcomes and cost-of-care for ICU patients.
Level correspondence of the K-theoretic I-function in Grassmann duality
Authors: Dong Hai , Wen Yaoxiong
Published: June 2022

In this paper, we prove a series of identities of the quasi-map K-theoretical I-functions with level structure between the Grassmannian and its dual Grassmannian. Those identities prove the quantum K-theory version mutation conjecture stated in [13]. Here we find an interval of levels within which two I-functions are the same, and on the boundary of that interval, two I-functions intertwine. We call this phenomenon the level correspondence in Grassmann duality.
Cross-flow oscillations of a circular cylinder with mechanically coupled rotation
Authors: Nitti A. , De Cillis G. , de Tullio M.D.
Published: June 2022

Flow-induced vibrations (FIV) of an elastically mounted circular cylinder are investigated by means of two-dimensional simulations. A mechanical coupling between cross-flow translation and rotation provides a single degree-of-freedom system in which the coupled rotational oscillations affect the fluid–structure dynamics. The structural response of this system is investigated exploring the design space spanned by reduced velocity, coupling radius and phase density ratio. The kinematic coupling introduces the rotation-induced shear layer modifications, as well as an equivalent inertia effect connected to the coupling force. Such a computational campaign is carried out by means of direct numerical simulations with immersed boundary forcing at a Reynolds number equal to 100. The investigated system exhibits the wake-body synchronisation features typical of lock-in for non-rotating cylinders. However, the kinematic coupling provides a novel FIV scenario, in which the oscillation amplitude is magnified in the locked configurations with respect to the forced rotation case. Furthermore, it is found that there a significant widening of the reduced velocity domain where the lock-in condition takes place. In view of the proposed analyses, it is determined that the coupled rotation guarantees the phase alignment between lift and displacement necessary to sustain the lock-in condition, making the oscillation amplitude grow indefinitely with the reduced velocity. This is inherently achieved due to the rotational shear layer and the added mass contribution, which prevent the exact match between oscillation frequency and system natural frequency in vacuum. The outcomes of this study might potentially lead to an innovative water energy harvester offering larger power outputs and extended optimal operating regions.
Denationalization in the Dominican Republic: Trapping Victims in the State’s Administrative Maze
Authors: Hunter Wendy , Reece Francesca
Published: June 2022

The Dominican Republic retroactively stripped thousands of Dominico-Haitians of their Dominican citizenship yet managed to defuse international opprobrium over time. After a direct assault on people’s citizenship status in 2013 provoked the human rights community’s ire, the DR employed administrative obstructionism to maneuver around human rights activism and institutions. Policies instituted in 2014 appeared to offer a pathway for Dominico-Haitians to reinstate their citizenship yet were so administratively onerous that most of the affected population remains effectively stateless. Administrative obstructionism makes for an elusive target of attack because it unfolds across a series of decisions over time, transfers responsibility from a highly visible leader to dispersed and faceless bureaucrats, and is exceedingly difficult to monitor. Administrative obstructionism drags out proceedings, causing media attention to wither. Because international forces face special challenges in countering this strategy, a strong domestic opposition movement is necessary to sustain pressure on a rights-violating government.
DETERMINATION OF THE TOTAL 14C CONCENTRATION OF WATER SAMPLES USING THE COD METHOD AND AMS
Authors: Molnár A , Molnár M , Veres M , Czébely A , Rinyu L , Rozmanitz P J , Janovics R
Published: June 2022

Radiocarbon (14C) is the one of the most important radionuclides released from the nuclear facilities to the environment. Currently, inorganic 14C is checked during regular environmental monitoring as part of the groundwater monitoring program of the Paks Nuclear Power Plant. Several studies have shown that organic 14C can be also an important and sensitive tool for detection of possible leakage of nuclear technological systems. For this reason, a wet oxidation method was developed for the accelerator mass spectrometry (AMS) 14C measurement technique to determine the 14C activity concentration of the total dissolved carbon content of water samples, coming from environmental monitoring wells. The overall efficiency of the oxidation was around 94 ± 5% for different types of tested organic compounds. The typical 14C background (1–2 pMC) is obtained by preparation of blank samples, which allows a detection level of around 5·10–5 Bq L–1. The activity of the organic fraction can be calculated using the formula presented in the study. The method was applied for water samples deriving from environmental monitoring wells of a pressurized-water reactor (PWR) type of NPP. The results of our investigations over the 14 different water samples around the Paks NPP show that DO14C contribution to the total 14C activity concentration was between 5–25%.
Politzer's test – but which one? A plea for standardisation of terms in otology
Authors: Mudry A , Young J R
Published: June 2022

Background

Politzer's tuning fork test is a little-known special examination with a chequered history.

Objective

This paper gives Politzer's original description, and explains how he intended it to be used.

Methods

The historiographical research in this study is based on primary references. Secondary documentation is only cited when it is necessary to substantiate any historical argument.

Results and conclusion

After the apparent disappearance of Politzer's tuning fork test from the otological scene in the 1950s, its consequent resurrection was not what it seemed. This story underlines the need for a standardisation of otological nomenclature, particularly when eponyms are used.
When Alphafold2 predictions go wrong for protein–protein complexes, is there something to be learnt?
Authors: Martin Juliette
Published: June 2022

In this short communication, I analyze cases of failed predictions for protein–protein complexes with Alphafold2, and show that they either point to erroneous annotation in the PDB or correct binding site regions.
SCIENCE, TECHNOLOGY, AND VALUE
Authors: Schmidtz David
Published: June 2022

Technological innovations and scientific discoveries do not occur in a vacuum but instead leave us needing to reimagine what we thought we knew about the human condition.
ALGORITHMIC ACCOUNTABILITY IN THE MAKING
Authors: Johnson Deborah G.
Published: June 2022

Algorithms are now routinely used in decision-making; they are potent components in decisions that affect the lives of individuals and the activities of public and private institutions. Although use of algorithms has many benefits, a number of problems have been identified with their use in certain domains, most notably in domains where safety and fairness are important. Awareness of these problems has generated public discourse calling for algorithmic accountability. However, the current discourse focuses largely on algorithms and their opacity. I argue that this reflects a narrow and inadequate understanding of accountability. I sketch an account of accountability that takes accountability to be a social practice constituted by actors, forums, shared beliefs and norms, performativity, and sanctions, and aimed at putting constraints on the exercise of power. On this account, algorithmic accountability is not yet constituted; it is in the making. The account brings to light a set of questions that must be addressed to establish it.
Pinangapalms revisited 20 years on: what can changes inPinangaspecies populations tell us about rainforest understory palm persistence?
Authors: Shapcott Alison , Slik J.W. Ferry , Rosli Roshanizah , Sukri Rahayu S.
Published: June 2022

Borneo is the centre of diversity of the palm genusPinanga. At least 13 understory species have been recorded in the Ulu Temburong National Park in Brunei, but little is known of their persistence. Changes in populations ofPinangaunderstory palms may be indicative of more widespread changes due to climate change, such as changes in rainfall, which may be important for the palm diversity in the protected area. However, we know little about the population dynamics of these palms, how persistent their populations are or if they behave similarly over long time frames. In 1998, populations of five co-occurring species ofPinangaat several locations in the Ulu Temburong National Park were documented. This project aimed to undertake a comprehensive resurvey of the original fivePinangapalm species populations in order to assess if they showed similar population changes across sites and species after two decades. Overall, most species maintained their population size in the surveyed region but not consistently among sites, and one species significantly declined in abundance. There was considerable variation in population growth rate (R) within and among species and sites that was significantly correlated with density and the percentage of multi-stemmed plants. There was evidence of pulsed recruitment in some species and or sites rather than steady or exponential patterns of population growth.
Nimble vessel cruises as a complementary platform for Southern Ocean biodiversity research: concept and preliminary results from the Belgica 121 expedition
Authors: Danis Bruno , Wallis Ben , Guillaumot Charlène , Moreau Camille , Pasotti Francesca , Heindler Franz M. , Robert Henri , Christiansen Henrik , Jossart Quentin , Saucède Thomas
Published: June 2022

The western Antarctic Peninsula is facing rapid environmental changes and many recent publications stress the need to gain new knowledge regarding ecosystems responses to these changes. In the framework of the Belgica 121 expedition, we tested the use of a nimble vessel with a moderate environmental footprint as an approach to tackle the urgent needs of the Southern Ocean research community in terms of knowledge regarding the levels of marine biodiversity in shallow areas and the potential impacts of retreating glaciers on this biodiversity in combination with increasing tourism pressure. We discuss the strengths and drawbacks of using a 75’ (23 m) sailboat in this research framework, as well as its sampling and environmental efficiency. We propose that the scientific community considers this approach to 1) fill specific knowledge gaps and 2) improve the general coherence of the research objectives of the Antarctic scientific community in terms of biodiversity conservation and the image that such conservation conveys to the general public.
Critical digital literacy in virtual exchange for ELT teacher education: An interpretivist methodology
Authors: Bilki Zeynep , Satar Müge , Sak Mehmet
Published: June 2022

Virtual exchange (VE) is an ideal venue for digital literacy skills development (Fuchs, Hauck & Müller-Hartmann, 2012) and for critical digital literacy (CDL) (Hauck, 2019). Yet literacy is a fluid, deictic term, the meaning of which is context dependent, and digital literacies need to be defined and conceptualised within a specific context. Recent CALL literature highlights the interest in CDL from various perspectives, but how CDL is conceptualised by the VE participants themselves is not explored. Participants of this study were 37 trainee English language teachers in the UK and Turkey who joined a 6-week VE. Their ongoing reflections on CDL were captured through reflective e-portfolio entries following each VE task. Thematic analysis revealed four components of CDL in this specific VE: (1) participants’ awareness of digital affordances for self-expression, (2) semiotic and interactional means to build connections, (3) ensuring inclusiveness of all community members, and (4) implications of socio-political contexts of each participant for meaning-making and interaction. We conclude that in future pedagogical implementations of VE, facilitators can foster trainee teachers’ CDL development through more closely guided and informed reflection on the four themes presented in this paper. As such, this study makes a novel contribution to our understanding of CDL in VE settings for ELT teacher education by offering a social semiotic second language acquisition orientation within an interpretivist paradigm.
Cropping systems alter plant volatile emissions in the field through soil legacy effects
Authors: Malone Shealyn C. , Menalled Fabian D. , Weaver David K. , Seipel Tim F. , Hofland Megan L. , Runyon Justin B. , Bourgault Maryse , Boss Darrin L. , Trowbridge Amy M.
Published: June 2022

Crops emit a variety of volatile organic compounds (VOCs) that serve as attractants or repellents for pests and their natural enemies. Crop rotations, off-farm chemical inputs, and mechanical and cultural tactics – collectively called cropping systems – alter soil nutrients, moisture content, and microbial communities, all of which have the potential to alter crop VOC emissions. Soil legacy effects of diversified cropping systems have been shown to enhance crop VOC emissions in greenhouse studies, but how they influence emissions under field conditions remains virtually unknown. To determine the effect of cropping systems on plant VOC emissions in the field, air samples were collected from the headspace of wheat (Triticum aestivum L. Judee) grown in simplified wheat-fallow rotations or diversified wheat-cover crop rotations where cover crops were terminated by grazing cattle. Across two growing seasons, wheat grown in rotation with fallow emitted greater amounts of Z-3-hexenyl acetate and β-ocimene, key attractants for wheat stem sawfly (Cephus cinctus Norton), a major pest of wheat. While overall VOC blends were relatively similar among cropping system during the first growing season, emissions varied substantially in the second year of this study where wheat grown in rotation with cover crops emitted substantially greater quantities of volatile compounds characteristic of abiotic stress. Below-average precipitation in the second growing season, in addition to reduced soil water content in cover crop rotations, suggests that cropping system effects on wheat VOCs may have been driven primarily by water availability, a major factor limiting crop growth in dryland agriculture. While the specific mechanisms driving changes in VOC emissions were not explicitly tested, this work shows that agricultural practices applied in one growing season can differentially influence crop VOC emissions in the next through soil legacy effects, illustrating additional avenues through which cropping systems may be leveraged to enhance pest management.
The dynamic nature of refugee children's resilience: a cohort study of Syrian refugees in Lebanon
Authors: Popham C. M. , McEwen F. S. , Karam E. , Fayyad J. , Karam G. , Saab D. , Moghames P. , Pluess M.
Published: June 2022

Aims

Children's responses to war and displacement are varied; many struggle, while others appear resilient. However, research into these outcomes disproportionately focuses on cross-sectional data in high-income countries. We aimed to (1) investigate change in resilience across two timepoints in a highly vulnerable sample of Syrian refugee children in Lebanon, and (2) explore predictors of their mental health problems across time.

Methods

In total, 982 Syrian child–caregiver dyads living in refugee settlements in Lebanon completed questionnaires via interview at baseline and follow-up one year later. We categorised children into groups based on their risk for mental health problems across both timepoints (stable high risk/SHR, deteriorating, improving, stable low risk) according to locally validated cut-offs on measures of post-traumatic stress disorder (PTSD), depression and behavioural problems. Analyses of covariance identified how the groups differed on a range of individual and socio-environmental predictors, followed up by cross-lagged panel models (CLPMs) to investigate the directionality of the relationships between significantly related predictors and symptoms.

Results

The sample showed a meaningful amount of change in mental health symptoms from baseline to follow-up. Over half (56.3%) of children met SHR criteria and 10.3% deteriorated over time, but almost one-quarter (24.2%) showed meaningful improvement, and 9.2% were consistently at low risk for mental health problems at both timepoints. Several predictors differentiated the groups, particularly social measures. According to CLPMs, maternal acceptance (β= −0.07) predicted child mental health symptoms over time. Self-esteem (β= −0.08), maternal psychological control (β= 0.10), child maltreatment (β= 0.09) and caregiver depression (β= 0.08) predicted child symptoms and vice versa (βse= −0.11,βb= 0.07,βmpc= 0.08,βcm= 0.1,βcd= 0.11). Finally, child symptoms predicted loneliness (β= 0.12), bullying (β= 0.07), perceived social support (β= −0.12), parent–child conflict (β= 0.13), caregiver PTSD (β= 0.07), caregiver anxiety (β= 0.08) and the perceived refugee environment (β= −0.09).

Conclusions

Our results show risk and resilience are dynamic, and the family environment plays a key role in children's response to war and displacement. Conversely, children also have a significant impact on the family environment and caregiver's own mental health. Interventions to promote resilience in refugee children should therefore consider family-wide mechanisms.
Verbal Behavior Analysis of Expert and Inexperienced Therapists Applying the Socratic Method
Authors: Pardo-Cebrián Rebeca , Calero-Elvira Ana , Guerrero-Escagedo María Cristina
Published: June 2022

The Socratic method, as an eminently verbal procedure, will be analyzed from a behavioral perspective in order to clarify how verbal conditioning works within. This work compares the verbalizations that expert and inexperienced therapists emit during Socratic method to find out which and why certain therapist verbalizations are most successful in changing client responses. The sample consisted of 113 Socratic method fragments from 18 cases, analyzed by observational methodology. The expert therapists had more than 6 years of experience, the inexperienced less than 2. Experts had fewer failure Socratic method fragments, but there were no differences in successful ones. The way of questioning had a different pattern: Inexperienced therapists suggested more the response, experts used more didactic verbalizations; also, experts used the aversive component more and contingently. The creation of guidelines based on functional description of verbal interaction and the need for novice psychologists training are some implications of these results.
Understanding Heavy Tails of Flood Peak Distributions
Authors: Merz Bruno , Basso Stefano , Fischer Svenja , Lun David , Blöschl Günter , Merz Ralf , Guse Björn , Viglione Alberto , Vorogushyn Sergiy , Macdonald Elena , Wietzke Luzie , Schumann Andreas
Published: June 2022

Statistical distributions of flood peak discharge often show heavy tail behavior, that is, extreme floods are more likely to occur than would be predicted by commonly used distributions that have exponential asymptotic behavior. This heavy tail behavior may surprise flood managers and citizens, as human intuition tends to expect light tail behavior, and the heaviness of the tails is very difficult to predict, which may lead to unnecessarily high flood damage. Despite its high importance, the literature on the heavy tail behavior of flood distributions is rather fragmented. In this review, we provide a coherent overview of the processes causing heavy flood tails and the implications for science and practice. Specifically, we propose nine hypotheses on the mechanisms causing heavy tails in flood peak distributions related to processes in the atmosphere, the catchment, and the river system. We then discuss to which extent the current knowledge supports or contradicts these hypotheses. We also discuss the statistical conditions for the emergence of heavy tail behavior based on derived distribution theory and relate them to the hypotheses and flood generation mechanisms. We review the degree to which the heaviness of the tails can be predicted from process knowledge and data. Finally, we recommend further research toward testing the hypotheses and improving the prediction of heavy tails.
Zhurong Rover Spots Evidence of Recent Liquid Water on Mars
Authors: Kornei Katherine
Published: June 2022

The Chinese rover identified hydrated minerals—likely associated with groundwater—in sediments dating to the Red Planet’s most recent geologic period.
Improved sampling scheme for LiDAR in Lissajous scanning mode
Authors: Wang Junya , Zhang Gaofei , You Zheng
Published: June 2022

MEMS light detection and ranging (LiDAR) is becoming an indispensable sensor in vehicle environment sensing systems due to its low cost and high performance. The beam scanning trajectory, sampling scheme and gridding are the key technologies of MEMS LiDAR imaging. In Lissajous scanning mode, this paper improves the sampling scheme, through which a denser Cartesian grid of point cloud data at the same scanning frequency can be obtained. By summarizing the rules of the Cartesian grid, a general sampling scheme independent of the beam scanning trajectory patterns is proposed. Simulation and experiment results show that compared with the existing sampling scheme, the resolution and the number of points per frame are both increased by 2 times with the same hardware configuration and scanning frequencies for a MEMS scanning mirror (MEMS-SM). This is beneficial for improving the point cloud imaging performance of MEMS LiDAR.
Differential grey matter structure in women with premenstrual dysphoric disorder: evidence from brain morphometry and data-driven classification
Authors: Dubol Manon , Stiernman Louise , Wikström Johan , Lanzenberger Rupert , Neill Epperson C. , Sundström-Poromaa Inger , Bixo Marie , Comasco Erika
Published: June 2022

Premenstrual dysphoric disorder (PMDD) is a female-specific condition classified in the Diagnostic and Statical Manual—5th edition under depressive disorders. Alterations in grey matter volume, cortical thickness and folding metrics have been associated with a number of mood disorders, though little is known regarding brain morphological alterations in PMDD. Here, women with PMDD and healthy controls underwent magnetic resonance imaging (MRI) during the luteal phase of the menstrual cycle. Differences in grey matter structure between the groups were investigated by use of voxel- and surface-based morphometry. Machine learning and multivariate pattern analysis were performed to test whether MRI data could distinguish women with PMDD from healthy controls. Compared to controls, women with PMDD had smaller grey matter volume in ventral posterior cortices and the cerebellum (Cohen’s d = 0.45–0.76). Region-of-interest analyses further indicated smaller volume in the right amygdala and putamen of women with PMDD (Cohen’s d = 0.34–0.55). Likewise, thinner cortex was observed in women with PMDD compared to controls, particularly in the left hemisphere (Cohen’s d = 0.20–0.74). Classification analyses showed that women with PMDD can be distinguished from controls based on grey matter morphology, with an accuracy up to 74%. In line with the hypothesis of an impaired top-down inhibitory circuit involving limbic structures in PMDD, the present findings point to PMDD-specific grey matter anatomy in regions of corticolimbic networks. Furthermore, the results include widespread cortical and cerebellar regions, suggesting the involvement of distinct networks in PMDD pathophysiology.
Clinical sequencing of soft tissue and bone sarcomas delineates diverse genomic landscapes and potential therapeutic targets
Authors: Nacev Benjamin A. , Sanchez-Vega Francisco , Smith Shaleigh A. , Antonescu Cristina R. , Rosenbaum Evan , Shi Hongyu , Tang Cerise , Socci Nicholas D. , Rana Satshil , Gularte-Mérida Rodrigo , Zehir Ahmet , Gounder Mrinal M. , Bowler Timothy G. , Luthra Anisha , Jadeja Bhumika , Okada Azusa , Strong Jonathan A. , Stoller Jake , Chan Jason E. , Chi Ping , D’Angelo Sandra P. , Dickson Mark A. , Kelly Ciara M. , Keohan Mary Louise , Movva Sujana , Thornton Katherine , Meyers Paul A. , Wexler Leonard H. , Slotkin Emily K. , Glade Bender Julia L. , Shukla Neerav N. , Hensley Martee L. , Healey John H. , La Quaglia Michael P. , Alektiar Kaled M. , Crago Aimee M. , Yoon Sam S. , Untch Brian R. , Chiang Sarah , Agaram Narasimhan P. , Hameed Meera R. , Berger Michael F. , Solit David B. , Schultz Nikolaus , Ladanyi Marc , Singer Samuel , Tap William D.
Published: June 2022

The genetic, biologic, and clinical heterogeneity of sarcomas poses a challenge for the identification of therapeutic targets, clinical research, and advancing patient care. Because there are > 100 sarcoma subtypes, in-depth genetic studies have focused on one or a few subtypes. Herein, we report a comparative genetic analysis of 2,138 sarcomas representing 45 pathological entities. This cohort is prospectively analyzed using targeted sequencing to characterize subtype-specific somatic alterations in targetable pathways, rates of whole genome doubling, mutational signatures, and subtype-agnostic genomic clusters. The most common alterations are in cell cycle control andTP53, receptor tyrosine kinases/PI3K/RAS, and epigenetic regulators. Subtype-specific associations includeTERTamplification in intimal sarcoma and SWI/SNF alterations in uterine adenosarcoma. Tumor mutational burden, while low compared to other cancers, varies between and within subtypes. This resource will improve sarcoma models, motivate studies of subtype-specific alterations, and inform investigations of genetic factors and their correlations with treatment response.
Sex-specific multi-level 3D genome dynamics in the mouse brain
Authors: Rocks Devin , Shukla Mamta , Ouldibbat Laila , Finnemann Silvia C. , Kalluchi Achyuth , Rowley M. Jordan , Kundakovic Marija
Published: June 2022

The female mammalian brain exhibits sex hormone-driven plasticity during the reproductive period. Recent evidence implicates chromatin dynamics in gene regulation underlying this plasticity. However, whether ovarian hormones impact higher-order chromatin organization in post-mitotic neurons in vivo is unknown. Here, we mapped the 3D genome of ventral hippocampal neurons across the oestrous cycle and by sex in mice. In females, we find cycle-driven dynamism in 3D chromatin organization, including in oestrogen response elements-enriched X chromosome compartments, autosomal CTCF loops, and enhancer-promoter interactions. With rising oestrogen levels, the female 3D genome becomes more similar to the male 3D genome. Cyclical enhancer-promoter interactions are partially associated with gene expression and enriched for brain disorder-relevant genes and pathways. Our study reveals unique 3D genome dynamics in the female brain relevant to female-specific gene regulation, neuroplasticity, and disease risk.
Excited state non-adiabatic dynamics of large photoswitchable molecules using a chemically transferable machine learning potential
Authors: Axelrod Simon , Shakhnovich Eugene , Gómez-Bombarelli Rafael
Published: June 2022

Light-induced chemical processes are ubiquitous in nature and have widespread technological applications. For example, photoisomerization can allow a drug with a photo-switchable scaffold such as azobenzene to be activated with light. In principle, photoswitches with desired photophysical properties like high isomerization quantum yields can be identified through virtual screening with reactive simulations. In practice, these simulations are rarely used for screening, since they require hundreds of trajectories and expensive quantum chemical methods to account for non-adiabatic excited state effects. Here we introduce adiabatic artificial neural network(DANN), based on diabatic states, to accelerate such simulations for azobenzene derivatives. The network is six orders of magnitude faster than the quantum chemistry method used for training. DANN is transferable to azobenzene molecules outside the training set, predicting quantum yields for unseen species that are correlated with experiment. We use the model to virtually screen 3100 hypothetical molecules, and identify novel species with high predicted quantum yields. The model predictions are confirmed using high-accuracy non-adiabatic dynamics. Our results pave the way for fast and accurate virtual screening of photoactive compounds.
Pre-existing antibody levels negatively correlate with antibody titers after a single dose of BBV152 vaccination
Authors: Das Suman , Singh Janmejay , Shaman Heena , Singh Balwant , Anantharaj Anbalagan , Sharanabasava Patil , Pandey Rajesh , Lodha Rakesh , Pandey Anil Kumar , Medigeshi Guruprasad R.
Published: June 2022

Many adults in India have received at least one dose of COVID-19 vaccine with or without a prior history SARS-CoV-2 infection. However, there is limited information on the effect of prior immunity on antibody response upon vaccination in India. As immunization of individuals continues, we aimed to assess whether pre-existing antibodies are further boosted by a single dose of BBV152, an inactivated SARS-CoV-2 vaccine, and, if these antibodies can neutralize SARS-CoV-2 Delta and Omicron variants. Here we show that natural infection during the second wave in 2021 led to generation of neutralizing antibodies against other lineages of SARS-CoV-2 including the Omicron variant, albeit at a significantly lower level for the latter. A single dose of BBV152 boosted antibody titers against the Delta and the Omicron variants but the antibody levels remained low against the Omicron variant. Boosting of antibodies showed negative correlation with baseline neutralizing antibody titers.
Microrheology of Pseudomonas aeruginosa biofilms grown in wound beds
Authors: Rahman Minhaz Ur , Fleming Derek F. , Wang Liyun , Rumbaugh Kendra P. , Gordon Vernita D. , Christopher Gordon F.
Published: June 2022

A new technique was used to measure the viscoelasticity of in vivo Pseudomonas aeruginosa biofilms. This was done through ex vivo microrheology measurements of in vivo biofilms excised from mouse wound beds. To our knowledge, this is the first time that the mechanics of in vivo biofilms have been measured. In vivo results are then compared to typical in vitro measurements. Biofilms grown in vivo are more relatively elastic than those grown in a wound-like medium in vitro but exhibited similar compliance. Using various genetically mutated P. aeruginosa strains, it is observed that the contributions of the exopolysaccharides Pel, Psl, and alginate to biofilm viscoelasticity were different for the biofilms grown in vitro and in vivo. In vitro experiments with collagen containing medium suggest this likely arises from the incorporation of host material, most notably collagen, into the matrix of the biofilm when it is grown in vivo. Taken together with earlier studies that examined the in vitro effects of collagen on mechanical properties, we conclude that collagen may, in some cases, be the dominant contributor to biofilm viscoelasticity in vivo.
Prediction of protected band edge states and dielectric tunable quasiparticle and excitonic properties of monolayer MoSi2N4
Authors: Wu Yabei , Tang Zhao , Xia Weiyi , Gao Weiwei , Jia Fanhao , Zhang Yubo , Zhu Wenguang , Zhang Wenqing , Zhang Peihong
Published: June 2022

The electronic structure of two-dimensional (2D) materials are inherently prone to environmental perturbations, which may pose significant challenges to their applications in electronic or optoelectronic devices. A 2D material couples with its environment through two mechanisms: local chemical coupling and nonlocal dielectric screening effects. The local chemical coupling is often difficult to predict or control experimentally. Nonlocal dielectric screening, on the other hand, can be tuned by choosing the substrates or layer thickness in a controllable manner. Therefore, a compelling 2D electronic material should offer band edge states that are robust against local chemical coupling effects. Here it is demonstrated that the recently synthesized MoSi2N4 is an ideal 2D semiconductor with robust band edge states protected from capricious environmental chemical coupling effects. Detailed many-body perturbation theory calculations are carried out to illustrate how the band edge states of MoSi2N4 are shielded from the direct chemical coupling effects, but its quasiparticle and excitonic properties can be modulated through the nonlocal dielectric screening effects. This unique property, together with the moderate band gap and the thermodynamic and mechanical stability of this material, paves the way for a range of applications of MoSi2N4 in areas including energy, 2D electronics, and optoelectronics.
Nondestructive identification of softness via bioinspired multisensory electronic skins integrated on a robotic hand
Authors: Qiu Ye , Sun Shenshen , Wang Xueer , Shi Kuanqiang , Wang Zhiqiang , Ma Xiaolong , Zhang Wenan , Bao Guanjun , Tian Ye , Zhang Zheng , Ding Hao , Chai Hao , Liu Aiping , Wu Huaping
Published: June 2022

Tactile sensing is essentially required for dexterous manipulation in robotic applications. Mimicking human perception of softness identification in a non-invasive fashion, thus achieving satisfactory interaction with fragile objects remains a grand challenge. Here, a scatheless measuring methodology based on the multisensory electronic skins to quantify the elastic coefficient of soft materials is reported. This recognition approach lies in the preliminary classification of softness by piezoelectric signals with a modified machine learning algorithm, contributing to an appropriate contact force assignment for subsequent quantitative measurements via strain sensing feedback. The integration of multifunctional sensing system allows the manipulator to hold capabilities of self-sensing and adaptive grasping motility in response to objects with the various softness (i.e., kPa-MPa). As a proof-of-concept demonstration, the biomimetic manipulator cooperates with the robotic arm to realize the intelligent sorting of oranges varying in freshness, paving the way for the development of microsurgery robots, human-machine interfacing, and advanced prosthetics.
Plant tissue characteristics of Miscanthus x giganteus
Authors: Pisani Oliva , Liebert Dan , Strickland Timothy C. , Coffin Alisa W.
Published: June 2022

As part of a study identifying relationships between environmental variables and insect distributions within a bioenergy crop, giant miscanthus (Miscanthus x giganteus) samples were collected in October 2016 at 33 locations within a field in southeast Georgia, USA. At each location, one plant sample was collected every 3 to 4 m along a 15 m transect, resulting in 5 replicates per sampling location. The plant samples were separated into leaves and stems, dried, and ground. The chemical composition of the ground material was assessed by measuring total carbon and nitrogen, total macro- and micronutrients (aluminum, arsenic, boron, calcium, cadmium, cobalt, chromium, copper, iron, potassium, magnesium, manganese, molybdenum, sodium, nickel, phosphorus, lead, sulfur, selenium, silicon, titanium, vanadium, and zinc) using Inductively Coupled Plasma with Optical Emission Spectroscopy (ICP-OES), and optical characteristics of the water extractable organic matter (WEOM) using UV-Visible and Fluorescence Excitation Emission Matrix (EEM) spectroscopy. This dataset will be useful to identify relationships between the chemical composition of giant miscanthus tissues and pest distributions within a bioenergy crop field.
Glacier thickness and ice volume of the Northern Andes
Authors: Van Wyk de Vries Maximillian , Carchipulla-Morales David , Wickert Andrew D. , Minaya Verónica G.
Published: June 2022

Tropical glacier melt provides valuable water to surrounding communities, but climate change is projected to cause the demise of many of these glaciers within the coming century. Understanding the future of tropical glaciers requires a detailed record of their thicknesses and volumes, which is currently lacking in the Northern Andes. We calculate present-day (2015–2021) ice-thicknesses for all glaciers in Colombia and Ecuador using six different methods, and combine these into multi-model ensemble mean ice thickness and volume maps. We compare our results against available field-based measurements, and show that current ice volumes in Ecuador and Colombia are 2.49 ± 0.25 km3and 1.68 ± 0.24 km3respectively. We detected no motion on any remaining ice in Venezuela. The overall ice volume in the region, 4.17 ± 0.35 km3, is half of the previous best estimate of 8.11 km3. These data can be used to better evaluate the status and distribution of water resources, as input for models of future glacier change, and to assess regional geohazards associated with ice-clad volcanoes.
Datasets for benchmarking antimicrobial resistance genes in bacterial metagenomic and whole genome sequencing
Authors: Raphenya Amogelang R. , Robertson James , Jamin Casper , de Oliveira Martins Leonardo , Maguire Finlay , McArthur Andrew G. , Hays John P.
Published: June 2022

Whole genome sequencing (WGS) is a key tool in identifying and characterising disease-associated bacteria across clinical, agricultural, and environmental contexts. One increasingly common use of genomic and metagenomic sequencing is in identifying the type and range of antimicrobial resistance (AMR) genes present in bacterial isolates in order to make predictions regarding their AMR phenotype. However, there are a large number of alternative bioinformatics software and pipelines available, which can lead to dissimilar results. It is, therefore, vital that researchers carefully evaluate their genomic and metagenomic AMR analysis methods using a common dataset. To this end, as part of the Microbial Bioinformatics Hackathon and Workshop 2021, a ‘gold standard’ reference genomic and simulated metagenomic dataset was generated containing raw sequence reads mapped against their corresponding reference genome from a range of 174 potentially pathogenic bacteria. These datasets and their accompanying metadata are freely available for use in benchmarking studies of bacteria and their antimicrobial resistance genes and will help improve tool development for the identification of AMR genes in complex samples.
Hairy surfaces by cold drawing leading to dense lawns of high aspect ratio hairs
Authors: Müllers Stefan , Florea-Hüring Mara , von Vacano Bernhard , Bruchmann Bernd , Rühe Jürgen
Published: June 2022

The surfaces of many organisms are covered with hairs, which are essential for their survival in a complex environment. The generation of artificial hairy surfaces from polymer materials has proven to be challenging as it requires the generation of structures with very high aspect ratios (AR). We report on a technique for the fabrication of surfaces covered with dense layers of very high AR nanoscale polymer hairs. To this, templates having pores with diameters of several hundred nanometers are filled with a polymer melt by capillary action. The polymer is then allowed to cool and the template is mechanically removed. Depending on the conditions employed, the formed structures can be a simple replica of the pore, or the polymer is deformed very strongly by cold drawing to yield in long hairs, with hair densities significantly up to 6,6 × 108 hairs/cm2 at AR of much higher than 200. The mechanism of hair formation is attributed to a delicate balance between the adhesion forces of the polymer in the pore and the yield force acting on it during mechanically demolding. We demonstrate how with very little effort and within a timescale of seconds unique topographies can be obtained, which can dramatically tailor the wetting properties of common polymers.
Towards interpretable, medically grounded, EMR-based risk prediction models
Authors: Twick Isabell , Zahavi Guy , Benvenisti Haggai , Rubinstein Ronya , Woods Michael S. , Berkenstadt Haim , Nissan Aviram , Hosgor Enes , Assaf Dan
Published: June 2022

Machine-learning based risk prediction models have the potential to improve patient outcomes by assessing risk more accurately than clinicians. Significant additional value lies in these models providing feedback about the factors that amplify an individual patient’s risk. Identification of risk factors enables more informed decisions on interventions to mitigate or ameliorate modifiable factors. For these reasons, risk prediction models must be explainable and grounded on medical knowledge. Current machine learning-based risk prediction models are frequently ‘black-box’ models whose inner workings cannot be understood easily, making it difficult to define risk drivers. Since machine learning models follow patterns in the data rather than looking for medically relevant relationships, possible risk factors identified by these models do not necessarily translate into actionable insights for clinicians. Here, we use the example of risk assessment for postoperative complications to demonstrate how explainable and medically grounded risk prediction models can be developed. Pre- and postoperative risk prediction models are trained based on clinically relevant inputs extracted from electronic medical record data. We show that these models have similar predictive performance as models that incorporate a wider range of inputs and explain the models’ decision-making process by visualizing how different model inputs and their values affect the models’ predictions.
TSP, a virulent Podovirus, can control the growth of Staphylococcus aureus for 12 h
Authors: Tabassum Rabia , Basit Abdul , Alvi Iqbal Ahmed , Asif Muhammad , ur Rehman Shafiq
Published: June 2022

Methicillin-resistant Staphylococcus aureus (MRSA) is a prevailing nosocomial pathogen that is increasingly isolated in community settings. It shows resistance against all beta-lactam drugs and has acquired mechanisms to resist other groups of antibiotics. To tackle this emerging issue of MRSA, there is an urgent need for antibiotic alternatives, and utilizing lytic bacteriophages is one of the most promising therapeutic approaches. In the present study, a lytic bacteriophage TSP was isolated from hospital wastewater against MRSA. The phage efficiently inhibited bacterial growth for up to 12 h at MOI of 1 and 10. TSP phage showed activity against various isolates of MRSA and MSSA, isolated from different clinical samples, with variable antibiotic susceptibility patterns. The bacteriophage TSP showed stability at varying temperatures (25 °C, 37 °C) and pH values (5–9), while its maximum storage stability was observed at 4 °C. It had a short latent period (20 min) and burst size of 103 ± 5pfu/infected cells. TSP genome sequence and restriction analysis revealed that its genome has a linear confirmation and length of 17,987 bp with an average GC content of 29.7%. According to comparative genomic analysis and phylogenetic tree,TSP phage can be considered a member of genus “P68viruses”. The strong lytic activity and short latent period in addition to its lytic nature makes it a good candidate for phage therapy against MRSA infections, if it proves to be effective in in-vivo studies.
Temporal mapping of derived high-frequency gene variants supports the mosaic nature of the evolution of Homo sapiens
Authors: Andirkó Alejandro , Moriano Juan , Vitriolo Alessandro , Kuhlwilm Martin , Testa Giuseppe , Boeckx Cedric
Published: June 2022

Large-scale estimations of the time of emergence of variants are essential to examine hypotheses concerning human evolution with precision. Using an open repository of genetic variant age estimations, we offer here a temporal evaluation of various evolutionarily relevant datasets, such as Homo sapiens-specific variants, high-frequency variants found in genetic windows under positive selection, introgressed variants from extinct human species, as well as putative regulatory variants specific to various brain regions. We find a recurrent bimodal distribution of high-frequency variants, but also evidence for specific enrichments of gene categories in distinct time windows, pointing to different periods of phenotypic changes, resulting in a mosaic. With a temporal classification of genetic mutations in hand, we then applied a machine learning tool to predict what genes have changed more in certain time windows, and which tissues these genes may have impacted more. Overall, we provide a fine-grained temporal mapping of derived variants in Homo sapiens that helps to illuminate the intricate evolutionary history of our species.
Remineralization of early enamel lesions with a novel prepared tricalcium silicate paste
Authors: Hamdi Kareem , Hamama Hamdi H. , Motawea Amira , Fawzy Amr , Mahmoud Salah Hasab
Published: June 2022

To evaluate the remineralization potential of prepared tricalcium silicate (TCS) paste compared to silver diamine fluoride-potassium iodide (SDF-KI) and casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) on artificial enamel lesions. Thirty permanent sound molars were collected for the study. After cleaning, root cutting, and applying acid-resistant nail varnish, leaving a 4 × 4 mm buccal window, the teeth were subjected to demineralization process. The teeth were divided into three treatment groups (n = 10). In each group, the teeth were sectioned buccolingually to obtain two halves (30 self-control and 30 experimental halves). The self-control halves were subjected to cross-sectional microhardness (CSMH), energy-dispersive X-ray spectroscopy at 50, 100, and 150 µm from the external enamel surface, and micromorphological analysis at the superficial enamel surface. The experimental halves were subjected to the same tests after 30 days of remineralization. Three-way analysis of variance (ANOVA) outcomes showed no significant difference in CSMH after treatment among the three different groups at the different levels (p > 0.05). Meanwhile, three-way ANOVA outcomes showed a significant difference in calcium/ phosphate ratio after treatment among the three different groups at the different levels. (p < 0.05). The tricalcium silicate paste used in this study showed potential remineralization in subsurface enamel lesions.