bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantum communication through devices with indefinite input-output direction
Authors: Liu Zixuan , Yang Ming , Chiribella Giulio
Published: March 2023

Certain quantum devices, such as half-wave plates and quarter-wave plates in quantum optics, are bidirectional, meaning that the roles of their input and output ports can be exchanged. Bidirectional devices can be used in a forward mode and a backward mode, corresponding to two opposite choices of the input-output direction. They can also be used in a coherent superposition of the forward and backward modes, giving rise to new operations with indefinite input-output direction. In this work we explore the potential of input-output indefiniteness for the transfer of classical and quantum information through noisy channels. We first formulate a model of communication from a sender to a receiver via a noisy channel used in indefinite input-output direction. Then, we show that indefiniteness of the input-output direction yields advantages over standard communication protocols in which the given noisy channel is used in a fixed input-output direction. These advantages range from a general reduction of noise in bidirectional processes, to heralded noiseless transmission of quantum states, and, in some special cases, to a complete noise removal. The noise reduction due to input-output indefiniteness can be experimentally demonstrated with current photonic technologies, providing a way to investigate the operational consequences of exotic scenarios characterised by coherent quantum superpositions of forward-time and backward-time processes.
Dynamic evolution of low-viscosity fuel particle distribution driven by constant flow
Authors: Yang Zhong-Kun , An Gao-Jun , Xu Xi-Meng , Zheng Zhe , Wang Yong-Xu , Xie Li-Feng , Zhang Dan , Li Bin
Published: March 2023

The effects of mass concentration and injection pressure on the atomization characteristics of low-viscosity fuel spray are studied in a constant-volume chamber. Microscopic spray parameters are measured by laser diffraction at different axial and radial positions downstream of the nozzle. The results show that the atomization effect is inhibited linearly with the increase of mass concentration. The increase of injection pressure promotes the droplet breakup. However, the trend gradually weakens and becomes more noticeable at high concentrations. Comparing with the concentration, the influence of the injection pressure on the atomization characteristics is dominant. Although low concentration and high injection pressure can promote the droplet breakup, they also increase the probability of droplet collision, resulting in droplet aggregation. This is more evident in low-viscosity fuels. The droplet size increases in the axial direction owing to the aggregation. However, the diameter decreases in the radial direction owing to the outward deflection of small droplets caused by air turbulence and entrainment. In addition, the high-velocity airflow significantly promotes the droplet breakup near the nozzle and spray axis regions and inhibits the aggregation effect. However, the lower-viscosity fuels keep smaller droplet sizes and better atomization in the whole spraying process, which is easier to realize than the higher-viscosity fuels. Overall, low concentration, high injection pressure, and low viscosity of fuel have beneficial effects on the droplet breakup. This is very important for improving the atomization effect of fuel.
MXene/poly(ionic liquid) porous composite membranes for systematized solar-driven interfacial steam generation
Authors: Khorsand Kheirabad Atefeh , Chang Jian , Zhang Miao , Yuan Jiayin
Published: March 2023

Herein, we established a synthetic route towards MXene/poly(ionic liquid) (PIL) composite porous membranes as a new platform of solar-thermal conversion materials. These membranes were made by a base-triggered ionic crosslinking process between a cationic PIL and a weak polyacid in solution in the presence of dispersed MXene nanosheets. A three-dimensionally interconnected porous architecture was formed with MXene nanosheets uniformly distributed within it. The unique characteristics of the as-produced composite membranes displays significant light-to-heat conversion and excellent performance for solar-driven water vapor generation. This facile synthetic strategy opens a new avenue for developing composite porous membranes as solar absorbers for the solar-driven water production from natural resources.
In-vitro and in-vivo wound healing studies of Ag@TiO2NRs/GG hydrogel film for skin tissue regeneration
Authors: Li Ganggang , Tan Xuejing , Zhao Wenwei , Muhamad A’srai Alina Irwana , Razali Mohd Hasmizam
Published: March 2023

One million cases of skin wounds, either closed or open wounds, necessitate wound treatments to improve the quality of life. In this study, gellan gum biopolymer (Ag@TiO2NRs/GG) hydrogel film with Ag loaded TiO2 nanorods was fabricated for wound healing dressing. The wound healing performance of Ag@TiO2WR/GG hydrogel was tested in vitro and in vivo to investigate its ability to regenerate skin tissue. FTIR, XRD, and SEM were used to examine the physical and chemical properties of prepared Ag@TiO2NRs/GG hydrogel film, as well as pure Ag and Ag@TiO2NRs. The FTIR spectra revealed the functional groups of Ag, TiO2NRs, GG, and their interactions. The hydrogel film was in an amorphous form, according to XRD analysis, due to the helical structure of GG and the presence of Ag and TiO2NRs in distinct phases. The SEM image shows agglomeration of Ag particles and elongated TiO2 nanorods, indicating that Ag@TiO2NRs were successfully incorporated onto GG hydrogel film. Human skin fibroblast cells (CRL2522) were used to study the in vitro wound healing of Ag@TiO2NRs/GG hydrogel film for cell viability and proliferation. After 72 h, ∼98,022 cells well−1 were counted, indicating that the Ag@TiO2NRs/GG was biocompatible and non-toxic. In vivo wound healing on Sprague Dawley rats revealed 100% wound healing after 14 days of treatment with Ag@TiO2NRs/GG hydrogel film. On a treated skin wound, ultrasound images revealed a thicker epidermis, clear dermis, and subcutis layer, indicating a positive correlation between wound healing and skin tissue regeneration.
Understanding the cause of sea level rise along coastal zone for 2005–2021
Authors: Yang Yuanyuan , Mu Dapeng , Zhong Min , Zhong Yulong , Yao Yanli
Published: March 2023

Understanding the coastal sea level budget (SLB) is essential to revealing the causes of sea level rise and predicting future sea level change. Here we present the coastal SLB based on multiple sets of sea level observations, including satellite altimetry, satellite gravimetry, and Argo floats over 2005 to 2021. The coastal zone is defined within 500 km from the coast and covered by all Argo products. We find that sea level observations enable a closure for the coastal SLB for 2005-2015. However, since 2016, the coastal SLB shows a substantially larger discrepancy, consistent with the global mean SLB. The coastal SLB is unclosed for 2005-2021, with a mean sea level rise of 4.06 ± 0.27 mm yr−1, a 0.74 ± 0.21 mm yr−1 rate for ocean mass, and a 2.27 ± 0.53 mm yr−1 for the steric component. Systematic Argo buoy salinity drift after 2016 is the main cause for the non-closure of coastal SLB over 2005-2021. Ignoring the suddenly unrealistic coastal salinity trends, the global coastal SLB from 2005 to 2021 is closed with a residual trend of 0.46 ± 0.63 mm yr−1. Our results confirm that the coastal 500 km range does not need to be deliberately masked and ignored in global SLB research.
The burden of Alzheimer’s disease and other types of dementia in the Middle East and North Africa region, 1990–2019
Authors: Safiri Saeid , Noori Maryam , Nejadghaderi Seyed Aria , Mousavi Seyed Ehsan , Sullman Mark J M , Araj-Khodaei Mostafa , Collins Gary S , Kolahi Ali-Asghar , Gharagozli Kurosh
Published: March 2023

Background

Alzheimer’s disease (AD) is the most common cause of dementia and this progressive neurological disorder is associated with substantial mortality and morbidity. We aimed to report the burden of AD and other types of dementia in the Middle East and North Africa (MENA) region, by age, sex and sociodemographic index (SDI), for the period 1990–2019.

Methods

publicly accessible data on the prevalence, death and disability-adjusted life years (DALYs) because of AD, and other types of dementia, were retrieved from the global burden of disease 2019 project for all MENA countries from 1990 to 2019.

Results

in 2019, the age-standardised point prevalence of dementia was 777.6 per 100,000 populations in MENA, which was 3.0% higher than in 1990. The age-standardised death and DALY rates of dementia were 25.5 and 387.0 per 100,000, respectively. In 2019, the highest DALY rate was observed in Afghanistan and the lowest rate was in Egypt. That same year, the age-standardised point prevalence, death and DALY rates increased with advancing age and were higher for females of all age groups. From 1990 to 2019, the DALY rate of dementia decreased with increasing SDI up to 0.4, then slightly increased up to an SDI of 0.75, followed by a decrease for the remaining SDI levels.

Conclusions

the point prevalence of AD and other types of dementia has increased over the past three decades, and in 2019, the corresponding regional burden was higher than the global average.
Comparison of hospitalization costs for the same adverse reaction associated with different medications
Authors: Alabbas Sama A , Jiang Rong , Au Anthony , Vu Michelle , Moore Von R , Cunningham Francesca E , Stroupe Kevin , Bounthavong Mark , Glassman Peter A , Good Chester B , Salone Cedric , Aspinall Sherrie L
Published: March 2023

Purpose

Costs of hospitalization due to severe adverse drug reactions (ADRs) were previously estimated within the Veterans Health Administration (VHA), but additional analyses are needed to infer potential interventions to mitigate these negative outcomes. The objective of this study was to compare specific adverse reaction–related hospitalization costs between medications with similar indications.

Methods

Mean hospitalization costs associated with the same ADR symptom were compared for different drugs with similar indications using adjusted generalized linear models with a Bonferroni correction for multiple comparisons as well as a gamma distribution.

Results

Overall, hospitalization costs between medications with similar indications were not significantly different for specific adverse reactions. However, gastrointestinal hemorrhage–associated costs were higher for warfarin versus nonsteroidal anti-inflammatory drugs (model estimate of mean cost, $18,114 [range of lower and upper model estimates, $12,522-$26,202] vs $14,255 [estimate range, $9,710-$20,929]). Similarly, the estimated mean hospitalization cost associated with angioedema was higher for losartan versus lisinopril or lisinopril/hydrochlorothiazide: $14,591 (range, $9467-$22,488) versus $8,935 (range, $6,301-$12,669) and $8,022 (range, $5,424-$11,865), respectively.

Conclusion

Although we found few differences in the cost of hospitalization when comparing drugs with similar indications and the same adverse reaction, there were specific drug-ADR pairs that merit attention and consideration of interventions to improve safe and appropriate medication use. Evaluation of the effect of those interventions on the incidence of ADRs is an area for future study.
Climate change-related growth improvements in a wide niche-breadth tree species across contrasting environments
Authors: Fajardo Alex , Gazol Antonio , Meynard Paulo Moreno , Mayr Christoph , Martínez Pastur Guillermo J , Peri Pablo L , Camarero J Julio
Published: March 2023

Background and Aims

The vulnerability and responsiveness of forests to drought are immensely variable across biomes. Intraspecific tree responses to drought in species with wide niche breadths that grow across contrasting climatically environments might provide key information regarding forest resistance and changes in species distribution under climate change. Using a species with an exceptionally wide niche breath, we tested the hypothesis that tree populations thriving in dry environments are more resistant to drought than those growing in moist locations.

Methods

We determined temporal trends in tree radial growth of 12 tree populations of Nothofagus antarctica (Nothofagaceae) located across a sharp precipitation gradient (annual precipitation of 500–2000 mm) in Chile and Argentina. Using dendrochronological methods, we fitted generalized additive mixed-effect models to predict the annual basal area increment as a function of year and dryness (De Martonne aridity index). We also measured carbon and oxygen isotope signals (and estimated intrinsic water-use efficiency) to provide potential physiological causes for tree growth responses to drought.

Key Results

We found unexpected improvements in growth during 1980–1998 in moist sites, while growth responses in dry sites were mixed. All populations, independent of site moisture, showed an increase in their intrinsic water-use efficiency in recent decades, a tendency that seemed to be explained by an increase in the photosynthetic rate instead of drought-induced stomatal closure, given that δ18O did not change with time.

Conclusions

The absence of drought-induced negative effects on tree growth in a tree species with a wide niche breadth is promising because it might relate to the causal mechanisms tree species possess to face ongoing drought events. We suggest that the drought resistance of N. antarctica might be attributable to its low stature and relatively low growth rate.
ProsmORF-pred: a machine learning-based method for the identification of small ORFs in prokaryotic genomes
Authors: Khanduja Akshay , Kumar Manish , Mohanty Debasisa
Published: March 2023

Small open reading frames (smORFs) encoding proteins less than 100 amino acids (aa) are known to be important regulators of key cellular processes. However, their computational identification remains a challenge. Based on a comprehensive analysis of known prokaryotic small ORFs, we have developed the ProsmORF-pred resource which uses a machine learning (ML)-based method for prediction of smORFs in the prokaryotic genome sequences. ProsmORF-pred consists of two ML models, one for initiation site recognition in nucleic acid sequences upstream of putative start codons and the other uses translated amino acid sequences to decipher functional protein like sequences. The nucleotide sequence-based initiation site recognition model has been trained using longer ORFs (>100 aa) in the same genome while the ML model for identification of protein like sequences has been trained using annotated smORFs from Escherichia coli. Comprehensive benchmarking of ProsmORF-pred reveals that its performance is comparable to other state-of-the-art approaches on the annotated smORF set derived from 32 prokaryotic genomes. Its performance is distinctly superior to other tools like PRODIGAL and RANSEPS for prediction of newly identified smORFs which have a length range of 10–30 aa, where prediction of smORFs has been a major challenge. Apart from identification of smORFs in genomic sequences, ProsmORF-pred can also aid in functional annotation of the predicted smORFs based on sequence similarity and genomic neighbourhood similarity searches in ProsmORFDB, a well-curated database of known smORFs. ProsmORF-pred along with its backend database ProsmORFDB is available as a user-friendly web server (http://www.nii.ac.in/prosmorfpred.html).
Desperation on the Battlefield, the Ethnic Security Dilemma, or Economic Competition? Mass Shootings in Chicago’s Gang Wars, 2010–20
Authors: Burke Patrick J
Published: March 2023

In this study examine the logic of gang-related mass shootings in Chicago between 2010 and 2020. I argue that gangs utilize mass shootings to win market share when demand for illegal drugs spikes. I also test two established theories of indiscriminate violence: ‘desperation on the battlefield’ and the ‘ethnic security dilemma’. To do so I construct an original dataset mainly using Freedom of Information Act responses. Using opioid overdose data to proxy for demand in drug markets, I find support for my theory in a series of linear fixed effects models. The ‘ethnic security dilemma’ also finds support. However, the two variables meant to proxy for ‘desperation’, search warrants and arrests of gang members for shootings, reduce gang-related mass shootings—the opposite of the predicted outcome. I conclude by discussing contributions to the existing literature, limitations and pathways for future research.
Assessment of the impact of a 10-MW grid-tied solar system on the Libyan grid in terms of the power-protection system stability
Authors: Alasali Feras , Saidi Abdelaziz Salah , El-Naily Naser , Alsmadi Othman , Khaleel Mohamed , Ghirani Ibrahim
Published: March 2023

The energy market in Libya is expected to face substantial changes in the next few years: electrical energy consumption will increase by 50% within the next 4 years. Therefore, there is a plan to gradually increase renewable energy sources in the power network by 2030 to 30%. Solar photovoltaic (PV) plants will play a significant role in the energy transition and the mix of energy sources in Libya. This article is a study conducted to investigate the challenges of power-flow management and power protection from integrating PV power plants into the Libyan power grid. In particular, a simulation model is built for the Kufra PV power plant (10 MW) with eight buses to assess the power network performance in terms of power quality such as voltage profile, power losses and harmonics. Furthermore, the impact of the PV plant on the short-circuit level and the power-protection system is presented under different operating conditions. The fault ride-through (FRT) is operated using standard ambient temperature and a wide range of irradiation intensity, and is verified by using the Libyan grid code. The results show that the integration of the PV plant into the grid has a significant impact on the short-circuit level and the FRT over the different fault levels and locations on the network. The initial period of the three-phase fault shows that the PV plant will be disconnected from the grid due to a decrease in the root mean square value voltages where the reactive and active power of the grid reach 938 MVAR and 261 MW, respectively. These results show that increasing the fault level will lead to an increase in injecting the active power. This work is considered the first extensive investigation into the challenges of modern power-flow management and power protection for the power network system in Libya.
Does aerobic scope influence geographical distribution of teleost fishes?
Authors: Nati Julie J H , Halsey Lewis G , Johnson Paul C D , Lindström Jan , Killen Shaun S
Published: March 2023

Many abiotic and biotic factors are known to shape species' distributions, but we lack understanding of how innate physiological traits, such as aerobic scope (AS), may influence the latitudinal range of species. Based on theoretical assumptions, a positive link between AS and distribution range has been proposed, but there has been no broad comparative study across species to test this hypothesis. We collected metabolic rate data from the literature and performed a phylogenetically informed analysis to investigate the influence of AS on the current geographical distributions of 111 teleost fish species. Contrary to expectations, we found a negative relationship between absolute latitude range and thermal peak AS in temperate fishes. We found no evidence for an association between thermal range of AS and the range of latitudes occupied for 32 species. Our main results therefore contradict the prevailing theory of a positive link between AS and distribution range in fish.
The Lexicographer’s Dream Audience: Dictionary Use among English Majors at a Slovenian University
Authors: Vrbinc Marjeta , Vrbinc Alenka , Farina Donna M T Cr
Published: March 2023

Interviews with undergraduate students from the University of Ljubljana, who are majoring in English and can be considered language specialists, investigated habits of dictionary use, look-up abilities, and perceptions of the utility and quality of definitions and illustrative examples. This contrasts with a parallel study (Farina et al. 2019) with undergraduates majoring in business and economics. Like the parallel study, this study was based on fourteen questions and nine contexts containing a clearly-marked common word used in an infrequent sense; participants had to locate the sense in a dictionary that, at the time of the studies, was the online Merriam–Webster Learner’s Dictionary, rebranded today as The Britannica Dictionary. Participants were asked to think aloud as they looked up words. Among other results, the study revealed that its participants, while they were linguistically-educated and experienced, did not fully grasp the complexity of presenting dictionary information online.
Recovering Racial Positioning in “White” Women's International Thought: Lady Kathleen Simon's International Abolitionist Crusade, 1927–1955
Authors: Napier Isabelle
Published: March 2023

The new field of history of women's international thought is part of, and gives further impetus to, the ongoing reckoning of international relations (IR) with the centrality of race and gender to the discipline. Scholars continue to recuperate a long inheritance of international thinkers concerned with race relations, colonial administration, and empire in nineteenth- and twentieth-century global political economies dependent on violent exploitation of peoples classified as inferior. This inheritance underscores that the politics of colonialism, war, humanitarianism, development, and decolonization have shaped and been shaped by processes of reinforcing and contesting racialized subject positions. Despite this, little attention has been paid to whiteness in histories of women's international thought. In this article, I recover the international thought of white British antislavery advocate and humanitarian Lady Kathleen Simon. I bring feminist and critical race scholarship to bear on Simon's writings and practice. Through her efforts to rouse a twentieth-century international abolitionist movement to emancipate those remaining enslaved in so-called backwards places, Simon played a consequential role in defending Ethiopia's occupation by fascist Italy from 1936 to 1941 and in arguing for continued European administration of Ethiopia after its liberation. In light of critiques of humanitarianism and of the role of white women in reproducing racial hierarchies in colonial and development contexts, I argue that recovery and analysis of the subject positions of historical women racialized as white is inextricable from the project of international intellectual history and from IR's continuing engagement with questions of gendered and racialized hierarchy and othering.
Philanthropic Foundations and Transnational Activist Networks: Ford and the Inter-American Institute of Human Rights
Authors: Gonzalez-Ocantos Ezequiel , Morcillo Laiz Álvaro
Published: March 2023

Foundations provide key funds for nongovernmental organizations. We know little about what they do for transnational activism or the mechanisms via which they seek/achieve influence. We carve a middle ground between those who see donors as supporting actors in transnational advocacy networks (TANs) and those who think they distort activism through impersonal market forces. Our negotiation-oriented approach looks at the micro-dynamics of donor–grantee relations. We argue that influence is a function of donors’ organizational characteristics. Only some, especially foundations, have the vision/means to shape grantees. However, internal complexity can cause coordination problems, complicating influence. Additionally, if many donors exist, recipients’ leverage increases. It does so too if their expertise is in short supply. Using archival evidence, we reconstruct how Ford tried to shape the Inter-American Human Rights Institute, a pillar of the region's human rights regime, and the factors conditioning success. For Ford, the Institute could play a role in a fledging TAN, but only if it downplayed its emphasis on research and directly engaged activists. Coupled with analyses of USAID’s relationship with the Institute and Ford's relationship with Americas Watch, we shed light on the activities of an important class of donor and illuminate foundations’ role in the development of TANs.
Genetic assessment improves conservation efforts for the critically endangered oceanic island endemic Hibiscus liliiflorus
Authors: Mashburn Brock , Jhangeer-Khan Reshad , Bégué Alfred , Tatayah Vikash , Olsen Kenneth M , Edwards Christine E
Published: March 2023

Hibiscus liliiflorus, endemic to the Indian Ocean island of Rodrigues, is one of the rarest plant species in the world; only 2 wild individuals remain. Previously, when 4 wild individuals remained, the Mauritian Wildlife Foundation (MWF) in Rodrigues propagated cuttings of them in their nursery, then planted seedlings produced in the nursery into 3 outplanted populations on the island. Our goals were to: 1) assess whether all 4 original wild genotypes are represented in the MWF nursery; 2) determine whether ex situ living collections at international botanical gardens maintain unique genotypes of H. liliiflorus; 3) assess whether nursery individuals have crossed or self-fertilized to produce seed and quantify their relative contributions to outplanted populations; and 4) provide recommendations for future conservation actions. We used a 2b-RADseq approach to produce 2,711 genome-wide single nucleotide polymorphisms (SNPs) from 98 samples. Genotype identity analysis, principal component analysis, and model-based clustering in STRUCTURE found 4 genotypes extant in Rodrigues but no unique genotypes in ex situ botanic garden collections. Only 3 genotypes are represented in the MWF nursery; the one remaining genotype is represented by an extant wild individual. Parentage analysis showed that seeds produced in the MWF nursery resulted from both self-fertilization and crossing between genotypes, a result supported by internal relatedness and hybrid index calculations. Each outplanted population is dominated by a subset of parental genotypes, and we propose actions to balance the parental contributions to outplanted populations. Our study highlights how genetic assessments of ex situ conservation projects help conserve critically endangered species.
Report of multiple high-grade gliomas in two patients with shared retained ATRX, wild-type IDH, losses of CDKN2A genes and alterations in the PTEN–PI3K axis
Authors: Khatchadourian Christopher , Guo Jin , Prasad Chaya J , Orlando Robert A , Parsa Cyrus
Published: March 2023

Solitary gliomas have been well described in the literature. Multiple gliomas, however, have not received the same notoriety, and as such further studies may be helpful in elucidating their unique clinicopathologic features and molecular basis. We present two patients, each with multiple high-grade gliomas, and describe their clinicopathologic and molecular characteristics in comparison with those reported in the literature in an attempt to better understand their shared tumorigenic mechanisms. Extensive molecular, FISH and genomic profiling studies detected multiple unique abnormalities in our two cases with shared molecular features of retained ATRX, wild-type IDH, losses of CDKN2A genes and alterations in the PTEN–PI3K Axis.
The Chlamydomonas reinhardtii chloroplast envelope protein LCIA transports bicarbonate in planta
Authors: Förster Britta , Rourke Loraine M , Weerasooriya Hiruni N , Pabuayon Isaiah C M , Rolland Vivien , Au Eng Kee , Bala Soumi , Bajsa-Hirschel Joanna , Kaines Sarah , Kasili Remmy W , LaPlace Lillian M , Machingura Marylou C , Massey Baxter , Rosati Viviana C , Stuart-Williams Hilary , Badger Murray R , Price G Dean , Moroney James V
Published: March 2023

LCIA (low CO2-inducible protein A) is a chloroplast envelope protein associated with the CO2-concentrating mechanism of the green alga Chlamydomonas reinhardtii. LCIA is postulated to be a HCO3– channel, but previous studies were unable to show that LCIA was actively transporting bicarbonate in planta. Therefore, LCIA activity was investigated more directly in two heterologous systems: an Escherichia coli mutant (DCAKO) lacking both native carbonic anhydrases and an Arabidopsis mutant (βca5) missing the plastid carbonic anhydrase βCA5. Neither DCAKO nor βca5 can grow in ambient CO2 conditions, as they lack carbonic anhydrase-catalyzed production of the necessary HCO3– concentration for lipid and nucleic acid biosynthesis. Expression of LCIA restored growth in both systems in ambient CO2 conditions, which strongly suggests that LCIA is facilitating HCO3– uptake in each system. To our knowledge, this is the first direct evidence that LCIA moves HCO3– across membranes in bacteria and plants. Furthermore, the βca5 plant bioassay used in this study is the first system for testing HCO3– transport activity in planta, an experimental breakthrough that will be valuable for future studies aimed at improving the photosynthetic efficiency of crop plants using components from algal CO2-concentrating mechanisms.
Rescheduling rehabilitation sessions with answer set programming
Authors: Cardellini Matteo , Dodaro Carmine , Galatà Giuseppe , Giardini Anna , Maratea Marco , Nisopoli Nicholas , Porro Ivan
Published: March 2023

The rehabilitation scheduling process consists of planning rehabilitation physiotherapy sessions for patients, by assigning proper operators to them in a certain time slot of a given day, taking into account several requirements and optimizations, e.g. patient’s preferences and operator’s work balancing. Being able to efficiently solve such problem is of upmost importance, in particular as a consequence of the COVID-19 pandemic that significantly increased rehabilitation’s needs. The problem has been recently successfully solved via a two-phase solution based on answer set programming (ASP). In this paper, we focus on the problem of rescheduling the rehabilitation sessions, which comes into play when the original schedule cannot be implemented, for reasons that involve the unavailability of operators and/or the absence of patients. We provide rescheduling solutions based on ASP for both phases, considering different scenarios. Results of experiments performed on real benchmarks, provided by ICS Maugeri, show that also the rescheduling problem can be solved in a satisfactory way. Finally, we present a web application that supports the usage of our solution.
Historical and Philosophical Considerations in Studying Psychopathology
Authors: Zachar Peter , Banicki Konrad , Aftab Awais
Published: March 2023

In this chapter, the authors trace a tug of war between adopting more descriptive versus more conjectural approaches to the study of psychopathology from the seventeenth century onward. The contrast between descriptive versus conjectural is somewhat relative. Statements which rely on shared background assumptions tend to be viewed as descriptions, while those that do not are viewed as conjectural. Throughout the history of psychopathology attempts to offer causal explanations have relied on conjecture hoping to extend our knowledge, but when conjecture was seen as going too far, there were calls to return to descriptions, on which there is more consensus. Recently, the descriptive psychopathology paradigm that was introduced in the DSM-III has been challenged by renewed calls for explaining disorders with respect to etiology and pathogenesis. Turning to causal explanations, the authors contrast production versus regularity accounts of causality. Production accounts tend to favor reducing mind to brain, whereas regularity accounts do not place a priori restrictions on which levels of analysis have genuine casual power. The authors also look at a recently proposed nonreductive perspective in the philosophy of mind, the 4E framework, in which the mind is seen as embodied, embedded, enactive, and extended. The chapter closes by examining the contrast between scientific realism and scientific anti-realism in the study of psychopathology, emphasizing the common ground between scientific realism and factor analytic models and describing some alternative anti-realist views.
The Research Domain Criteria Project: Integrative Translation for Psychopathology
Authors: Cuthbert Bruce N. , Miller Gregory A. , Sanislow Charles , Vaidyanathan Uma
Published: March 2023

This chapter provides an introduction to the Research Domain Criteria (RDoC) project. RDoC is a framework for psychopathology research created in 2009 by the US National Institute of Mental Health in order to foster innovative research that transcends the reliance on current disorder categories in studying mental illness. RDoC takes a translational approach that considers psychopathology in terms of deviations in normal dimensions of functioning (such as cognitive processes or motivational systems) that often reflect transdiagnostic effects across multiple disorder classes. The framework calls for studies that integrate multiple data types (e.g., behavioral, physiological, and self-report measures) and emphasizes developmental trajectories and the impact of various environmental influences. Fundamental issues regarding relevant philosophy of science issues are discussed, and selected recent studies are reviewed that illustrate exemplars of research designs. The conclusion briefly summarizes RDoC’s current status and potential future directions.
Developmental Psychopathology
Authors: Cicchetti Dante
Published: March 2023

Developmental psychopathology is an integrative scientific discipline focused on individual biological and psychological adaptation and maladaptation in the context of developmental change. Developmental psychopathology owes the emergence and coalescence of its framework to many historically based disciplines including, but not limited to neuroscience, ethology, sociology, psychiatry, pediatrics, and clinical, developmental, experimental and physiological psychology. A developmental analysis presupposes change and novelty, highlights the important role of timing in the organization of behavior, underscores multiple determinants, and cautions against expecting invariant relations between causes and outcomes. From a developmental psychopathology framework, mental disorders are conceived as being dynamic and should be studied from an interdisciplinary perspective and a multiple levels of analysis approach. The continuation and elaboration of multiple levels of analysis longitudinal studies within and across disciplines interested in typical and atypical development not only will enhance the science of developmental psychopathology, but also will increase the benefits derived for individuals with high-risk conditions or mental disorders, families, and society as a whole.
Diagnosis, Comorbidity, and Psychopathology of Substance-Related Disorders
Authors: Brumback Ty , Brown Sandra A.
Published: March 2023

This chapter describes substance use disorders (SUDs) beginning with the categorical diagnostic categories and the identified etiological risk factors for developing SUDs before moving to the various outcomes among those with SUDs, including comorbid psychopathology. Alcohol use disorder is the most common SUD and, as such, is a focal point of this chapter, although the authors also describe the growing literature related to other SUDs and comorbidities. The chapter represents a biopsychosocial understanding of SUDs, which recognizes that the factors contributing to the onset of SUDs must reflect the complexity of the disorders and include biological underpinnings (e.g., genetic predispositions and physiological factors), psychological contributions (e.g., psychopathology that may contribute to and exacerbate SUDs), and social factors (e.g., peer influences and early life stressors) that influence the heterogenous etiological pathways and symptom profiles of patients with SUDs.
Social Functioning and Schizophrenia
Authors: Hooley Jill M. , DeCross Stephanie N.
Published: March 2023

Schizophrenia is associated with significant problems in social functioning. This chapter provides an overview of the literature concerning social functioning in schizophrenia, tracing progress over time. It begins by considering the nature of social exchanges and describing the social problems experienced by patients with schizophrenia, then discusses factors associated with better or worse social functioning, focusing particularly on the role of gender, and positive and negative symptoms. The authors review the literature concerning social impairments in the premorbid phases of the illness as well as in those at risk for developing the disorder. Following a review of early and foundational literature, the authors turn attention toward newer areas of research and evolving conceptualization of schizophrenia, highlighting current understanding of the complex interplay of social cognition, social motivation, and social anhedonia and discussing evidence on the altered neurobiological bases for these processes. Finally, they consider the role of the patient’s social environment for the course of schizophrenia, ending with a discussion of treatment options available to help patients and their families function more effectively in the face of this illness.
Sleep and Circadian Rhythm Disorders
Authors: Bisdounis Lampros , Kyle Simon D. , Saunders Kate E. A. , Hill Elizabeth A. , Espie Colin A.
Published: March 2023

Sleep and circadian rhythm disorders are highly prevalent and impairing, yet they are often misdiagnosed and undertreated. This chapter covers such disorders presenting either as independent conditions or as comorbid diagnoses with other psychiatric disorders. First, an overview is provided of the fundamental principles, assessment tools, and nosology systems in sleep medicine. Subsequent sections focus specifically on the etiology, assessment, and evidence-based treatment of the following conditions: insomnia disorder, delayed and advanced circadian phase disorders, irregular sleep–wake rhythm disorder, non–24-hour sleep–wake rhythm disorder, narcolepsy, hypersomnolence disorder, and parasomnias. These represent the sleep and circadian rhythm disorders that are most commonly encountered by mental health practitioners. The final section highlights sleep and circadian disturbances in the context of four other psychiatric disorders: depression, anxiety, bipolar disorder, and schizophrenia.
Psychopathy and Antisocial Personality Disorder
Authors: Patrick Christopher J. , Drislane Laura E. , Bertoldi Bridget M. , Lowman Kelsey L.
Published: March 2023

Psychopathy and antisocial personality disorder (ASPD) have been of long-standing interest to clinicians and researchers due to their serious detrimental effects on both individuals and society as a whole. This chapter begins with an overview of historical writings that served as the foundation for modern conceptualizations of psychopathy and ASPD. Next, the chapter describes the main inventories for assessing psychopathy in use today and discusses how these various inventories differ from one another and how they relate to ASPD and other conditions in the official psychiatric nosology (the DSM-5). The chapter also summarizes findings regarding their neurobiological correlates. Following this, the authors describe an integrative conceptual-empirical framework—the triarchic model—for characterizing relations among different psychopathy measures and organizing what is known about their clinical and neurobiological correlates. The chapter then considers how the three constructs of the triarchic model—boldness, meanness, and disinhibition—are represented in the dimensional system for personality pathology within the DSM-5 and how they interface with the Hierarchical Taxonomy of Psychopathology (HiTOP), a new dimensional framework for psychopathology as a whole. Finally, the authors discuss how the triarchic model can be used to guide developmental research on psychopathy and coordinate further research on the role of neurobiological systems and processes in psychopathy.
Specific targeting of plasmids with Argonaute enables genome editing
Authors: Esyunina Daria , Okhtienko Anastasiia , Olina Anna , Panteleev Vladimir , Prostova Maria , Aravin Alexei A , Kulbachinskiy Andrey
Published: March 2023

Prokaryotic Argonautes (pAgos) are programmable nucleases involved in cell defense against invading DNA. In vitro, pAgos can bind small single-stranded guide DNAs to recognize and cleave complementary DNA. In vivo, pAgos preferentially target plasmids, phages and multicopy genetic elements. Here, we show that CbAgo nuclease from Clostridium butyricum can be used for genomic DNA engineering in bacteria. We demonstrate that CbAgo loaded with plasmid-derived guide DNAs can recognize and cleave homologous chromosomal loci, and define the minimal length of homology required for this targeting. Cleavage of plasmid DNA at an engineered site of the I-SceI meganuclease increases guide DNA loading into CbAgo and enhances processing of homologous chromosomal loci. Analysis of guide DNA loading into CbAgo also reveals off-target sites of I-SceI in the Escherichia coli genome, demonstrating that pAgos can be used for highly sensitive detection of double-stranded breaks in genomic DNA. Finally, we show that CbAgo-dependent targeting of genomic loci with plasmid-derived guide DNAs promotes homologous recombination between plasmid and chromosomal DNA, depending on the catalytic activity of CbAgo. Specific targeting of plasmids with Argonautes can be used to integrate plasmid-encoded sequences into the chromosome thus enabling genome editing.
RNA interactome capture in Escherichia coli globally identifies RNA-binding proteins
Authors: Stenum Thomas Søndergaard , Kumar Ankith D , Sandbaumhüter Friederike A , Kjellin Jonas , Jerlström-Hultqvist Jon , Andrén Per E , Koskiniemi Sanna , Jansson Erik T , Holmqvist Erik
Published: March 2023

RNA-binding proteins (RPBs) are deeply involved in fundamental cellular processes in bacteria and are vital for their survival. Despite this, few studies have so far been dedicated to direct and global identification of bacterial RBPs. We have adapted the RNA interactome capture (RIC) technique, originally developed for eukaryotic systems, to globally identify RBPs in bacteria. RIC takes advantage of the base pairing potential of poly(A) tails to pull-down RNA–protein complexes. Overexpressing poly(A) polymerase I in Escherichia coli drastically increased transcriptome-wide RNA polyadenylation, enabling pull-down of crosslinked RNA–protein complexes using immobilized oligo(dT) as bait. With this approach, we identified 169 putative RBPs, roughly half of which are already annotated as RNA-binding. We experimentally verified the RNA-binding ability of a number of uncharacterized RBPs, including YhgF, which is exceptionally well conserved not only in bacteria, but also in archaea and eukaryotes. We identified YhgF RNA targets in vivo using CLIP-seq, verified specific binding in vitro, and reveal a putative role for YhgF in regulation of gene expression. Our findings present a simple and robust strategy for RBP identification in bacteria, provide a resource of new bacterial RBPs, and lay the foundation for further studies of the highly conserved RBP YhgF.
Structures, activity and mechanism of the Type IIS restriction endonuclease PaqCI
Authors: Kennedy Madison A , Hosford Christopher J , Azumaya Caleigh M , Luyten Yvette A , Chen Minyong , Morgan Richard D , Stoddard Barry L
Published: March 2023

Type IIS restriction endonucleases contain separate DNA recognition and catalytic domains and cleave their substrates at well-defined distances outside their target sequences. They are employed in biotechnology for a variety of purposes, including the creation of gene-targeting zinc finger and TAL effector nucleases and DNA synthesis applications such as Golden Gate assembly. The most thoroughly studied Type IIS enzyme, FokI, has been shown to require multimerization and engagement with multiple DNA targets for optimal cleavage activity; however, details of how it or similar enzymes forms a DNA-bound reaction complex have not been described at atomic resolution. Here we describe biochemical analyses of DNA cleavage by the Type IIS PaqCI restriction endonuclease and a series of molecular structures in the presence and absence of multiple bound DNA targets. The enzyme displays a similar tetrameric organization of target recognition domains in the absence or presence of bound substrate, with a significant repositioning of endonuclease domains in a trapped DNA-bound complex that is poised to deliver the first of a series of double-strand breaks. PaqCI and FokI share similar structural mechanisms of DNA cleavage, but considerable differences in their domain organization and quaternary architecture, facilitating comparisons between distinct Type IIS enzymes.
Delineation of complex gene expression patterns in single cell RNA-seq data with ICARUS v2.0
Authors: Jiang Andrew , You Linya , Snell Russell G , Lehnert Klaus
Published: March 2023

Complex biological traits and disease often involve patterns of gene expression that can be characterised and examined. Here we present ICARUS v2.0, an update to our single cell RNA-seq analysis web server with additional tools to investigate gene networks and understand core patterns of gene regulation in relation to biological traits. ICARUS v2.0 enables gene co-expression analysis with MEGENA, transcription factor regulated network identification with SCENIC, trajectory analysis with Monocle3, and characterisation of cell-cell communication with CellChat. Cell cluster gene expression profiles may be examined against Genome Wide Association Studies with MAGMA to find significant associations with GWAS traits. Additionally, differentially expressed genes may be compared against the Drug-Gene Interaction database (DGIdb 4.0) to facilitate drug discovery. ICARUS v2.0 offers a comprehensive toolbox of the latest single cell RNA-seq analysis methodologies packed into an efficient, user friendly, tutorial style web server application (accessible at https://launch.icarus-scrnaseq.cloud.edu.au/) that enables single cell RNA-seq analysis tailored to the user's dataset.
Marine natural products and derivatives
Authors: Avhad Ashwini B , Bhangale Charushila J
Published: March 2023

Objectives

There are many reasons why marine resources are currently being examined extensively. One of the causes is that 70% of the earth’s surface is covered by oceans. From marine resources, some natural products and their derivatives are derived. These marine natural products are produced by the following organisms: marine invertebrates, marine algae and marine microbes are the three main biological classes. An overview of the marine natural products (MNPs) industry is presented, along with a current list of medications that the FDA has approved as well as those that are undergoing clinical trials and could be regarded as MNP derivatives.

Methods

Secondary metabolites from marine organisms such as snails, tunicates, sponges, soft corals and mollusks have been extracted to produce bio active compounds, which have sparked the creation of new classes of therapeutic agents. Marine life is a significant source of structurally diverse and biologically active secondary metabolites.

Key findings

It is observed that marine source is one of the powerful way of producing products that are natural and effective.

Conclusion

Some commercially available preparations treat diseases like HIV, cancer and various skin conditions using their collected resources.