bluuebunny/crossref_metadata_2025 huggingface dataset:
Maximum sustainable yield as a reference point in the presence of fishing effort that follows an ideal free distribution
Authors: Gillis Darren M. , Koscielny Jonah , Blanz Benjamin
Published: November 2023

The concept of maximum sustainable yield (MSY), and the underlying Schaefer model, remain relevant in fisheries management today in spite of past difficulties. However, this model is often applied without the consideration of the spatial structure or dynamics of fishing activities. We expand the Schaefer model to account for multiple fishing sites and fishing activities (effort) that follow an ideal free distribution (IFD, a form of Nash equilibrium) driven by exploitation. We explore this conceptual model using both analytical and numerical solutions. MSY across the fishery is unaffected by the spatial structure when fishing is allocated independently within sites. However, in other cases IFD effort dynamics depress MSY and modify the values of associated reference points. The game theoretic aspect of fleet dynamics should be considered in the use of MSY as a management reference point or during the application of the Schaefer model to data‐limited fisheries.
Invasive earthworms modulate native plant trait expression and competition
Authors: Schwarz Rike , Eisenhauer Nico , Ferlian Olga , Maestre Fernando. T. , Rosenbaum Benjamin , Uthe Henriette , Thouvenot Lise
Published: November 2023

Biological invasions have major impacts on a variety of ecosystems and threaten native biodiversity. Earthworms have been absent from northern parts of North America since the last ice age, but non‐native earthworms were recently introduced there and are now being spread by human activities. While past work has shown that plant communities in earthworm‐invaded areas change towards a lower diversity mainly dominated by grasses, the underlying mechanisms related to changes in the biotic interactions of the plants are not well understood. Here, we used a trait‐based approach to study the effect of earthworms on interspecific plant competition and aboveground herbivory. We conducted a microcosm experiment in a growth chamber with a full‐factorial design using three plant species native to northern North American deciduous forests, Poa palustris (grass), Symphyotrichum laeve (herb) and Vicia americana (legume), either growing in monoculture or in a mixture of three. These plant community treatments were crossed with earthworm (presence or absence) and herbivore (presence or absence) treatments. Eight out of the fourteen above‐ and belowground plant functional traits studied were significantly affected by earthworms, either by a general effect or in interaction with plant species identity, plant diversity level and/or herbivore presence. Earthworms increased the aboveground productivity and the number of inflorescences of the grass P. palustris. Further, earthworms and herbivores together affected root tissue density of P. palustris and the specific leaf area of V. americana. In this study, earthworm presence gave a competitive advantage to the grass species P. palustris by inducing changes in plant functional traits. Our results suggest that invasive earthworms can alter competitive and multitrophic interactions of plants, shedding light on some of the mechanisms behind invasive earthworm‐induced plant community changes in northern North America forests.
Overexpression of OsACL5 triggers environmentally‐dependent leaf rolling and reduces grain size in rice
Authors: Mai Huafu , Qin Tian , Wei Huan , Yu Zhen , Pang Gang , Liang Zhiman , Ni Jiansheng , Yang Haishan , Tang Haiying , Xiao Lisi , Liu Huili , Liu Taibo
Published: November 2023

Major polyamines include putrescine, spermidine, spermine and thermospermine, which play vital roles in growth and adaptation against environmental changes in plants. Thermospermine (T‐Spm) is synthetised by ACL5. The function of ACL5 in rice is still unknown. In this study, we used a reverse genetic strategy to investigate the biological function of OsACL5. We generated several knockout mutants by pYLCRISPR/Cas9 system and overexpressing (OE) lines of OsACL5. Interestingly, the OE plants exhibited environmentally‐dependent leaf rolling, smaller grains, lighter 1000‐grain weight and reduction in yield per plot. The area of metaxylem vessels of roots and leaves of OE plants were significantly smaller than those of WT, which possibly caused reduction in leaf water potential, resulting in leaf rolling with rise in the environmental temperature and light intensity and decrease in humidity. Additionally, the T‐Spm contents were markedly increased by over ninefold whereas the ethylene evolution was reduced in OE plants, suggesting that T‐Spm signalling pathway interacts with ethylene pathway to regulate multiple agronomic characters. Moreover, the osacl5 exhibited an increase in grain length, 1000‐grain weight, and yield per plot. OsACL5 may affect grain size via mediating the expression of OsDEP1, OsGS3 and OsGW2. Furthermore, haplotypes analysis indicated that OsACL5 plays a conserved function on regulating T‐Spm levels during the domestication of rice. Our data demonstrated that identification of OsACL5 provides a theoretical basis for understanding the physiological mechanism of T‐Spm which may play roles in triggering environmentally dependent leaf rolling; OsACL5 will be an important gene resource for molecular breeding for higher yield.
Presidential hawkishness, domestic popularity, and diplomatic normalization
Authors: Kim James D.
Published: November 2023

When does the United States normalize its diplomatic relations with its adversaries? This article introduces a theory of diplomatic normalization, focusing on the interaction between the hawkishness of presidents and their domestic popularity. I argue that dovish presidents are more likely to pursue normalization when their domestic approval ratings plummet, as this makes them shift their priorities toward policies they find themselves more comfortable and confident handling. Doves are less likely to pursue normalization when they enjoy high popularity, so as not to jeopardize favorable public support. In contrast, hawkish presidents typically do not support normalization, regardless of their domestic standing, as it does not align with their top policy priorities. The exception arises in the rare instance of a president with an exceptionally high degree of hawkishness who is able to pursue reconciliation without losing his support. I test my theoretical expectations using data on U.S. presidents' latent hawkishness and their diplomatic normalization decisions from 1950 to 2005. The empirical evidence supports all hypotheses, underscoring the importance of understanding the interaction between a leader's personal attributes and the domestic political climate when studying foreign policy decisions.
Machines meet humans on the social road: Risk implications
Authors: Liu Peng
Published: November 2023

Human drivers and machine drivers (i.e., automated vehicles or AVs) will share roads and interact with each other, creating mixed traffic. In this perspective, we develop two mental models about them and their social interactions, aiming to understand the risk implications of AVs and mixed traffic. Based on Mental Model I (i.e., machine drivers are superior drivers without human weaknesses), many simulation‐based safety assessments, which often overlook or oversimplify human‐AV social interactions, have predicted significant safety benefits when machine drivers interact with or replace human drivers. In contrast, Mental Model II considers human and machine drivers as heterogeneous and incompatible, suggesting that their interactions may lead to unexpected and occasionally negative outcomes, particularly in imminent mixed traffic. This perspective gains support from recent comparative empirical studies that employ various methods such as survey experiments, driving simulators, test‐tracks, on‐road observations, and AV accident analysis. These studies provide initial evidence of emerging traffic risks arising from human‐AV social interactions, including human drivers’ aggression and road rage toward AVs, human drivers exploiting AVs, AVs exerting negative peer influences on human drivers, and their incompatibility increasing human drivers’ challenges in joining mixed traffic and thus risky behaviors. We propose specific suggestions to mitigate problematic human‐AV social interactions and the associated emerging risks.
The Islamic State and the independence referendum: The role of foreign policy in maintaining the de facto Kurdish entity in Iraq
Authors: Sadoon Hajar Bashir
Published: November 2023

The onslaught of the Islamic State of Iraq and Syria (hereafter ISIS) on the Kurdishde factoentity in Iraq in 2014 and the independence referendum in 2017 constituted two important episodes that impacted on the foreign policy of the Kurdish entity in multiple ways. This article analyzes and describes the foreign policies of the entity during and after these two episodes until the end of 2022. It attempts to answer the following two questions: How did the ISIS offensive briefly change the priorities of the Kurdish entity's leadership in terms of its foreign policy goals? Secondly, how did the independence referendum in the Kurdistan Region of Iraq and the subsequent events shape the foreign policy priorities of the Kurdish entity in Iraq? Through conducting interviews with high‐level Kurdish politicians and using recently published secondary source materials, this article argues that foreign policy and paradiplomacy played vital roles in the preservation of the KRI during these two very tough periods and that the Kurdish entity had to alter its domestic policy goals to achieve its foreign policy aims and ensure the survival of the Kurdish facto entity in Iraq.
An Organizational Sociology of Education: Using Structural, Network, and Ecological Perspectives to Study Schools
Authors: Trinidad Jose Eos
Published: November 2023

Highlighting changes in education and organizational theorizing since the 1950s, this review integrates three perspectives for an organizational sociology of education. The structural perspective focuses on how the formal organization of resources, relationships, and information can influence student outcomes and inequalities through opportunities to learn. The network perspective highlights the role of informal interactions and interpretation as well as social and cultural capital to bring about changes. The ecological perspective illustrates how schools are affected by other schools (horizontal dimension), the educational bureaucracy (vertical dimension), and organizations outside schools (community dimension). An organizational perspective can concretize often abstract sociological topics on stratification, social reproduction, and socialization. The perspective can also reconceptualize often individualistic views on contemporary education issues like student well‐being, teacher shortage, racial inequalities, and school politics. The review ends with a discussion on how to incorporate these organizational perspectives and how they can complement current studies in education, sociology, and public policy.
The accessibility analysis of multiple public facilities in the central urban areas based on multi‐transportation modes: A study in Chengdu
Authors: Zhang Menghan , Li Zhenpei , Peng Hao
Published: November 2023

With the rapid development of social economy in Chengdu, it is of great significance to analyze the accessibility of a public facilities resources, and services in respective regions for the spatial planning of public facilities and the optimization of urban construction in Chengdu. Most existing studies only consider the accessibility of a single public facility under a single transportation mode studying facilities at the same level. In this research, with the consideration of all these factors mentioned above, an improved 3‐step floating catchment area (3SFCA) model of multi‐transportation modes is introduced to analyze the accessibility and spatial distribution of multiple types of public facilities under multiple traffic modes. The new model classifies the grade of public facilities and calculates the service accessibility of public facilities under the driving, public transport, cycling, and walking modes in the five dimensions of education, medical care, commerce, transportation, and leisure in the central urban areas of Chengdu. Through the comparative analysis of multiple models, we found that the improved 3SFCA can more accurately evaluate the accessibility of all dimensions of public facilities in central urban areas of Chengdu. The accessibility of compound public facilities in the central city is excellent. With the gradual expansion to the outward areas, the diversity and accessibility of compound public facilities gradually decreases. Furthermore, the accessibility distribution of public facilities in the study area is not balanced. The accessibility between the central urban areas and the marginal areas differs greatly and the spatial differentiation is substantial.
On a body‐switching argument in defence of the immateriality of human nature
Authors: Fatoorchi Pirooz
Published: November 2023

In an earlier paper in Theoria, I discussed an argument based on the idea of “soul‐switching” that attempted to undermine the immaterialist account of human beings. The present paper deals with a parity argument against that argument in which the idea of “body‐switching” plays a pivotal role. I call these two arguments, that have been reported by Razi (d. 1210), respectively “the soul‐switching argument” and “the body‐switching argument”. After some introductory remarks, section 2 of the paper describes the structure of the latter argument. Section 3 considers some philosophical discussions in the ancient, modern, and contemporary eras in which the idea of body‐switching (or some similar conception) plays a major role. In the following section 4, some criticisms of the argument are discussed and a general response that is meant to cover a broad range of objections is considered. This paper shows that the body‐switching argument reported by Razi is a methodological antecedent of several contemporary arguments in defence of substance dualism.
Melatonin confers tolerance to nitrogen deficiency through regulating MdHY5 in apple plants
Authors: Gao Tengteng , Liu Xiaomin , Xu Shuo , Yu Xi , Zhang Danni , Tan Kexin , Zhou Yi , Jia Xumei , Zhang Zhijun , Ma Fengwang , Li Chao
Published: November 2023

Nitrogen (N) is an essential nutrient for crop growth and development, significantly influencing both yield and quality. Melatonin (MT), a known enhancer of abiotic stress tolerance, has been extensively studied. However, its relationship with nutrient stress, particularly N deficiency, and the underlying regulatory mechanisms of MT on N absorption remain unclear. In this study, exogenous MT treatment was found to improve the tolerance of apple plants to N deficiency. Apple plants overexpressing the MT biosynthetic gene N‐acetylserotonin methyltransferase 9 (MdASMT9) were used to further investigate the effects of endogenous MT on low‐N stress. Overexpression of MdASMT9 improved the light harvesting and heat transfer capability of apple plants, thereby mitigating the detrimental effects of N deficiency on the photosynthetic system. Proteomic and physiological data analyses indicated that MdASMT9 overexpression enhanced the trichloroacetic acid cycle and positively modulated amino acid metabolism to counteract N‐deficiency stress. Additionally, both exogenous and endogenous MT promoted the transcription of MdHY5, which in turn bound to the MdNRT2.1 and MdNRT2.4 promoters and activated their expression. Notably, MT‐mediated promotion of MdNRT2.1 and MdNRT2.4 expression through regulating MdHY5, ultimately enhancing N absorption. Taken together, these findings shed light on the association between MdASMT9‐mediated MT biosynthesis and N absorption in apple plants under N‐deficiency conditions.
Dynamic transcriptome landscape of maize pericarp development
Authors: Zhang Jihong , Yue Yang , Hu Mingjian , Yi Fei , Chen Jian , Lai Jinsheng , Xin Beibei
Published: November 2023

As a maternal tissue, the pericarp supports and protects for other components of seed, such as embryo and endosperm. Despite the importance of maize pericarp in seed, the genome‐wide transcriptome pattern throughout maize pericarp development has not been well characterized. Here, we developed RNA‐seq transcriptome atlas of B73 maize pericarp development based on 21 samples from 5 days before fertilization (DBP5) to 32 days after fertilization (DAP32). A total of 25 346 genes were detected in programming pericarp development, including 1887 transcription factors (TFs). Together with pericarp morphological changes, the global clustering of gene expression revealed four developmental stages: undeveloped, thickening, expansion and strengthening. Coexpression analysis provided further insights on key regulators in functional transition of four developmental stages. Combined with non‐seed, embryo, endosperm, and nucellus transcriptome data, we identified 598 pericarp‐specific genes, including 75 TFs, which could elucidate key mechanisms and regulatory networks of pericarp development. Cell wall related genes were identified that reflected their crucial role in the maize pericarp structure building. In addition, key maternal proteases or TFs related with programmed cell death (PCD) were proposed, suggesting PCD in the maize pericarp was mediated by vacuolar processing enzymes (VPE), and jasmonic acid (JA) and ethylene‐related pathways. The dynamic transcriptome atlas provides a valuable resource for unraveling the genetic control of maize pericarp development.
The monotonicity and convexity of the incompressible rotational cavity flow
Authors: Cheng Jianfeng , Pei Zhenlei
Published: November 2023

This paper is concerned with the monotonicity and convexity of the incompressible rotational cavity flow past a fixed obstacle. More precisely, we first establish the single intersection property of the free boundary by the Serrin's under–over theorem, and prove the monotonicity of the free boundary with respect to the obstacle. If the obstacle is concave to the fluid, it is proved that the free boundary is convex to the fluid.
Educación, tecnologías y agencias en tiempos de virtualidad forzada
Authors: Taboada María Beatriz
Published: November 2023

El trabajo aborda experiencias docentes en contextos de virtualidad forzada de emergencia por COVID-19 en Argentina, a partir de testimonios obtenidos mediante entrevistas. El análisis propuesto recupera aportes teórico-metodológicos del análisis del discurso, así como la noción de cronotopo para dar cuenta del modo en que los testimonios explicitan la interdependencia entre espacio y tiempo en las experiencias educativas transitadas. Los discursos permiten reconstruir agencias que sustentan prácticas didácticas situadas y tensionadas por desafíos contextuales diversos, entre los que se destacan posibilidades limitadas de acceso a equipamiento y conectividad, así como el despliegue de prácticas compensatorias para intentar superar dificultades emergentes.
La pared ausente. Rupturas y desplazamientos del aula en pandemia
Authors: Bravo Úrsula , Dussel Inés
Published: November 2023

El uso de las paredes del aula forma parte de prácticas pedagógicas arraigadas, pero escasamente interrogadas. En este artículo de investigación abordamos las transformaciones de estas prácticas durante la enseñanza remota de emergencia (ERE) de veinte profesores provenientes de ocho escuelas primarias chilenas durante la pandemia. Realizamos un estudio cualitativo con sensibilidad etnográfica que incluyó entrevistas e inventarios del material digital elaborado por ellos. Los resultados muestran que los docentes tendieron a centrarse en el traspaso de información, quedando interrumpidas interacciones que decían valorar. Indagar los desplazamientos hacia las tecnologías digitales puede ayudar a comprender mejor los vínculos entre presencialidad y virtualidad.
Static Stability of Planar Contacting Systems: Analytical Treatment in Euclidean Space
Authors: Dan Alinjar , Rama Krishna K. , Saha S. K.
Published: November 2023

This paper gives an exact theory in Euclidean space for studying the static stability of planar rigid systems held by one or more frictional and frictionless contacts under gravity. Static stability analysis deals with determining the feasible locations of the center of gravity (CG) which ensure stability. The analysis is performed here in two steps—finding the equilibrium region and finding the stability region as a subset of the equilibrium region. The stability region is determined through the analytical treatment of an elegant geometric characterization. These results are also verified through elegant geometric reasoning based on curvature theory in-plane kinematics. In the end, stability analyses of some physical systems containing generic contacting curves are illustrated, and the results are presented with physical interpretations.
Effect of varying threading dislocation densities on the optical properties of InGaN/GaN quantum wells with intentionally created V-shaped pits
Authors: Zhang Kaitian , Hu Chenxi , Thirupakuzi Vangipuram Vijay Gopal , Meng Lingyu , Chae Christopher , Zhu Menglin , Hwang Jinwoo , Kash Kathleen , Zhao Hongping
Published: November 2023

The effect of varying threading dislocation densities on the internal quantum efficiencies (IQEs) of InGaN quantum wells (QWs), with and without intentionally created “V-pits,” is reported here. InGaN QW samples grown on GaN-on-sapphire templates with threading dislocation densities of <1 × 108 and <1 × 109 cm−2 are compared, with and without GaN/InGaN superlattice (SL) layers incorporated to intentionally open up the threading dislocation cores and form large-size “V-pits.” The formation of “V-pits” is confirmed by cross-sectional transmission electron microscopy to initiate from threading dislocations in the SL layers. The densities of the pits are confirmed by plan-view SEM to agree with the substrate threading dislocation densities. The experimental room temperature IQEs of the “V-pit” QW samples are enhanced to 15% ± 1% compared to 6% ± 2% for conventional QW samples. Both conventional and “V-pit” samples show insensitivity to the magnitude of the dislocation densities with respect to IQE performance, while the “V-pit” samples show shifts in the peak emission wavelengths compared to the conventional samples, attributed to strain modulation. This study provides additional understanding of the causes of the observed insensitivity of the IQEs to different threading dislocation densities.
Window into the mind: Advanced handheld spectroscopic eye-safe technology for point-of-care neurodiagnostic
Authors: Banbury Carl , Harris Georgia , Clancy Michael , Blanch Richard J. , Rickard Jonathan James Stanley , Goldberg Oppenheimer Pola
Published: November 2023

Traumatic brain injury (TBI), a major cause of morbidity and mortality worldwide, is hard to diagnose at the point of care with patients often exhibiting no clinical symptoms. There is an urgent need for rapid point-of-care diagnostics to enable timely intervention. We have developed a technology for rapid acquisition of molecular fingerprints of TBI biochemistry to safely measure proxies for cerebral injury through the eye, providing a path toward noninvasive point-of-care neurodiagnostics using simultaneous Raman spectroscopy and fundus imaging of the neuroretina. Detection of endogenous neuromarkers in porcine eyes’ posterior revealed enhancement of high–wave number bands, clearly distinguishing TBI and healthy cohorts, classified via artificial neural network algorithm for automated data interpretation. Clinically, translating into reduced specialist support, this markedly improves the speed of diagnosis. Designed as a hand-held cost-effective technology, it can allow clinicians to rapidly assess TBI at the point of care and identify long-term changes in brain biochemistry in acute or chronic neurodiseases.
Expression of the transcription factor Klf6 by thymic epithelial cells is required for thymus development
Authors: Malin Justin , Martinez-Ruiz Gustavo Ulises , Zhao Yongge , Shissler Susannah C. , Cowan Jennifer E. , Ding Yi , Morales-Sanchez Abigail , Ishikawa Masaki , Lavaert Marieke , Das Arundhoti , Butcher Donna , Warner Andrew C. , Kallarakal Melissa , Chen Jingqiu , Kedei Noemi , Kelly Michael , Brinster Lauren R. , Allman David , Bhandoola Avinash
Published: November 2023

Thymic epithelial cells (TEC) control T cell development and play essential roles in establishing self-tolerance. By using
Foxn1-Cre
–driven ablation of
Klf6
gene in TEC, we identified
Klf6
as a critical factor in TEC development.
Klf6
deficiency resulted in a hypoplastic thymus—evident from fetal stages into adulthood—in which a dramatic increase in the frequency of apoptotic TEC was observed. Among cortical TEC (cTEC), a previously unreported cTEC population expressing the transcription factor Sox10 was relatively expanded. Within medullary TEC (mTEC), mTEC I and Tuft-like mTEC IV were disproportionately decreased.
Klf6
deficiency altered chromatin accessibility and affected TEC chromatin configuration. Consistent with these defects, naïve conventional T cells and invariant natural killer T cells were reduced in the spleen. Late stages of T cell receptor–dependent selection of thymocytes were affected, and mice exhibited autoimmunity. Thus, Klf6 has a prosurvival role and affects the development of specific TEC subsets contributing to thymic function.
Very high-energy gamma-ray emission beyond 10 TeV from GRB 221009A
Authors:   The LHAASO Collaboration
Published: November 2023

The highest-energy gamma-rays from gamma-ray bursts (GRBs) have important implications for their radiation mechanism. Here we report the detection of gamma-rays up to 13 teraelectronvolts from the brightest GRB 221009A by the Large High Altitude Air-shower Observatory (LHAASO). The LHAASO-KM2A detector registered more than 140 gamma-rays with energies above 3 teraelectronvolts during 230 to 900 seconds after the trigger. The intrinsic energy spectrum of gamma-rays can be described by a power-law after correcting for extragalactic background light absorption. Such a hard spectrum challenges the synchrotron self-Compton scenario of relativistic electrons for the afterglow emission above several teraelectronvolts. Observations of gamma-rays up to 13 teraelectronvolts from a source with a measured redshift of
z
= 0.151 hints more transparency in intergalactic space than previously expected. Alternatively, one may invoke new physics such as Lorentz invariance violation or an axion origin of very high-energy signals.
Reconstructing visual illusory experiences from human brain activity
Authors: Cheng Fan L. , Horikawa Tomoyasu , Majima Kei , Tanaka Misato , Abdelhack Mohamed , Aoki Shuntaro C. , Hirano Jin , Kamitani Yukiyasu
Published: November 2023

Visual illusions provide valuable insights into the brain’s interpretation of the world given sensory inputs. However, the precise manner in which brain activity translates into illusory experiences remains largely unknown. Here, we leverage a brain decoding technique combined with deep neural network (DNN) representations to reconstruct illusory percepts as images from brain activity. The reconstruction model was trained on natural images to establish a link between brain activity and perceptual features and then tested on two types of illusions: illusory lines and neon color spreading. Reconstructions revealed lines and colors consistent with illusory experiences, which varied across the source visual cortical areas. This framework offers a way to materialize subjective experiences, shedding light on the brain’s internal representations of the world.
Contezolid can replace linezolid in a novel combination with bedaquiline and pretomanid in a murine model of tuberculosis
Authors: Almeida Deepak , Li Si-Yang , Lee Jin , Hafkin Barry , Mdluli Khisimuzi , Fotouhi Nader , Nuermberger Eric L.
Published: November 2023

Contezolid is a new oxazolidinone with
in vitro
and
in vivo
activity against
Mycobacterium tuberculosis
comparable to that of linezolid. Pre-clinical and clinical safety studies suggest it may be less toxic than linezolid, making contezolid a potential candidate to replace linezolid in the treatment of drug-resistant tuberculosis. We evaluated the dose-ranging activity of contezolid, alone and in combination with bedaquiline and pretomanid, and compared it with linezolid at similar doses, in an established BALB/c mouse model of tuberculosis. Contezolid had an MIC of 1 µg/mL, similar to linezolid, and exhibited similar bactericidal activity in mice. Contezolid-resistant mutants selected
in vitro
had 32- to 64-fold increases in contezolid MIC and harbored mutations in the
mce3R
gene. These mutants did not display cross-resistance to linezolid. Our results indicate that contezolid has the potential to replace linezolid in regimens containing bedaquiline and pretomanid and likely other regimens.
Viral infections and pathogenesis of glaucoma: a comprehensive review
Authors: Ahmad Faraz , Deshmukh Nikhil , Webel Aaron , Johnson Sandra , Suleiman Ayman , Mohan Rajiv R. , Fraunfelder Frederick , Singh Pawan Kumar
Published: November 2023

Glaucoma is a leading cause of irreversible blindness worldwide, caused by the gradual degeneration of retinal ganglion cells and their axons. While glaucoma is primarily considered a genetic and age-related disease, some inflammatory conditions, such as uveitis and viral-induced anterior segment inflammation, cause secondary or uveitic glaucoma. Viruses are predominant ocular pathogens and can impose both acute and chronic pathological insults to the human eye. Many viruses, including herpes simplex virus, varicella-zoster virus, cytomegalovirus, rubella virus, dengue virus, chikungunya virus, Ebola virus, and, more recently, Zika virus (ZIKV) and severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), have been associated with sequela of either primary or secondary glaucoma. Epidemiological and clinical studies suggest the association between these viruses and subsequent glaucoma development. Despite this, the ocular manifestation and sequela of viral infections are not well understood. In fact, the association of viruses with glaucoma is considered relatively uncommon in part due to underreporting and/or lack of long-term follow-up studies. In recent years, literature on the pathological spectrum of emerging viral infections, such as ZIKV and SARS-CoV-2, has strengthened this proposition and renewed research activity in this area. Clinical studies from endemic regions as well as laboratory and preclinical investigations demonstrate a strong link between an infectious trigger and development of glaucomatous pathology. In this article, we review the current understanding of the field with a particular focus on viruses and their association with the pathogenesis of glaucoma.
Measuring beta-lactam minimum inhibitory concentrations in
Staphylococcus aureus
in the clinical microbiology laboratory: pinning the tail on the donkey
Authors: Sakoulas George , Nizet Victor
Published: November 2023

Significant shortcomings have been identified in standard methods of susceptibility testing in bacteriological media, not only because the media fails to recapitulate the
in vivo
environment, but susceptibility testing itself fails to capture sub-MIC effects that significantly attenuate bacterial virulence properties. Until susceptibility testing conditions better recapitulate the
in vivo
environment, attempts to establish the quantitative relevance of beta-lactam MIC using current clinical microbiology standards in
Staphylococcus aureus
infections will likely prove unsuccessful.
Peroxisome dynamics determines host-derived ROS accumulation and infectious growth of the rice blast fungus
Authors: Zhang Jun , Li Huimin , Gu Wangliu , Zhang Kexin , Liu Xinyu , Liu Muxing , Yang Leiyun , Li Gang , Zhang Zhengguang , Zhang Haifeng
Published: November 2023

During the early stages of host-pathogen interaction, the production of reactive oxygen species (ROS) in host cells is a critical strategy to halt the spread of pathogens. Pathogens have to minimize the deleterious effects of host-generated ROS for successful invasion. However, the underlying mechanism remains largely elusive. Here, we report that a peroxisomal 3-ketoacyl-CoA thiolase of rice blast fungus
Magnaporthe oryzae
, MoKat2, functions in host ROS homeostasis likely through regulating fungal peroxisome morphology during infection.
M. oryzae
peroxisome elongates in response to ROS stress, and this is attributed to the function of peroxisome localized MoKat2. MoKat2 forms homodimer
in vivo
while the homodimer is dissociated into monomer in response to host-derived ROS. The MoKat2 monomer binds to peroxisome membranes through its amphipathic helices to control peroxisome elongation, resulting in host ROS depletion and subsequent
M. oryzae
invasion in rice cells. Our findings shed light on the interplay between pathogenic peroxisome dynamics and host ROS accumulation, expanding the crucial role of organelle-mediated infection in plant-microbe interactions.

IMPORTANCE

The interplay between plant and pathogen is a dynamic process, with the host’s innate defense mechanisms serving a crucial role in preventing infection. In response to many plant pathogen infections, host cells generate the key regulatory molecule, reactive oxygen species (ROS), to limit the spread of the invading organism. In this study, we reveal the effects of fungal peroxisome dynamics on host ROS homeostasis, during the rice blast fungus
Magnaporthe oryzae
infection. The elongation of the peroxisome appears contingent upon ROS and links to the accumulation of ROS within the host and the infectious growth of the pathogen. Importantly, we identify a peroxisomal 3-ketoacyl-CoA thiolase, MoKat2, responsible for the elongation of the peroxisome during the infection. In response to host-derived ROS, the homodimer of MoKat2 undergoes dissociation to bind peroxisome membranes for peroxisome elongation. This process, in turn, inhibits the accumulation of host ROS, which is necessary for successful infection. Overall, our study is the first to highlight the intricate relationship between fungal organelle dynamics and ROS-mediated host immunity, extending the fundamental knowledge of pathogen-host interaction.
Complete genome sequence of the pandrug-resistant
Vibrio cholerae
strain KBR06 isolated from a cholera patient in Bangladesh
Authors: Kabir Md. Mohiuddin , Imam Md. Rayhan , Farzana Zinat , Hossain Chowdhury Faiz
Published: November 2023

Vibrio cholerae
poses a serious hazard to global health and causes cholera disease in humans. Here, we present the full-genome sequence of a pandrug-resistant
V. cholerae
strain KBR06 isolated from a cholera patient in Bangladesh that exhibited intermediate resistance to only two antibiotics out of 39 among 14 antibiotic categories.
The interplay between the polar growth determinant DivIVA, the segregation protein ParA, and their novel interaction partner PapM controls the
Mycobacterium smegmatis
cell cycle by modulation of DivIVA subcellular distribution
Authors: Matusiak Izabela , Strzałka Agnieszka , Wadach Patrycja , Gongerowska-Jac Martyna , Szwajczak Ewa , Szydłowska-Helbrych Aleksandra , Kepplinger Bernhard , Pióro Monika , Jakimowicz Dagmara
Published: November 2023

Bacterial chromosome segregation is facilitated by the ParABS system. The ParB protein binds centromere-like
parS
sequences and forms nucleoprotein complexes. These nucleoprotein complexes are segregated by the dynamic ATPase ParA. In mycobacteria, ParA also interacts with the polar growth determinant DivIVA (Wag31). This interaction was earlier shown not only to facilitate the segregation of ParB complexes but also to affect cell extension. Here, we identify an additional partner of ParA in
Mycobacterium smegmatis
, named PapM. Using
E. coli
-based analysis, we show that PapM likewise interacts with DivIVA and that the tripartite interaction of ParA-PapM-DivIVA is phosphorylation dependent: ParA binding to DivIVA is diminished, while PapM binding is promoted upon phosphorylation of DivIVA. The presence of PapM enhances the dissociation of ParA from the DivIVA complex upon its phosphorylation. Studies of
M. smegmatis
mutant strains reveal that altered PapM levels influence chromosome segregation and cell length. The elimination of PapM affects ParA dynamics. Furthermore, ParA and, to a lesser extent, PapM modulate the subcellular distribution of DivIVA. Altogether, our studies show that the tripartite interplay between ParA-DivIVA and PapM controls the switch between cell division and cell elongation and, in this way, affects the mycobacterial cell cycle.

IMPORTANCE

The genus of
Mycobacterium
includes important clinical pathogens (
M. tuberculosis
). Bacteria of this genus share the unusual features of their cell cycle such as asymmetric polar cell elongation and long generation time. Markedly, control of the mycobacterial cell cycle still remains not fully understood. The main cell growth determinant in mycobacteria is the essential protein DivIVA, which is also involved in cell division. DivIVA activity is controlled by phosphorylation, but the mechanism and significance of this process are unknown. Here, we show how the previously established protein interaction partner of DivIVA in mycobacteria, the segregation protein ParA, affects the DivIVA subcellular distribution. We also demonstrate the role of a newly identified
M. smegmatis
DivIVA and ParA interaction partner, a protein named PapM, and we establish how their interactions are modulated by phosphorylation. Demonstrating that the tripartite interplay affects the mycobacterial cell cycle contributes to the general understanding of mycobacterial growth regulation.
Impact of contrasting poultry exposures on human, poultry, and wastewater antibiotic resistomes in Bangladesh
Authors: Williams Alexander D. , Rousham Emily , Neal Andrew L. , Amin Mohammed Badrul , Hobman Jon L. , Stekel Dov , Islam Mohammad Aminul
Published: November 2023

Interactions between humans, animals, and the environment are considered critical foci for addressing antimicrobial resistance (AMR). However, One Health data on AMR in low- and middle-income countries are presently scarce. Using metagenomics, we investigated whether and how the fecal antibiotic resistomes of humans are influenced by exposure to intensive and non-intensively reared poultry within contrasting settings of urban wet markets (
n
= 13) and rural households (
n
= 7) in Bangladesh. We also considered poultry (
n
= 10) and wastewater (
n
= 10) resistomes in these settings. We found that occupational poultry exposures did not significantly alter the human fecal resistome. In contrast, macrolide-lincosamide-streptogramin and streptothricin antibiotic resistance genes (ARGs) were enriched in poultry from urban wet markets relative to rural household chickens. Wastewater had the highest ARG richness, though this was only partially explained by poultry cecal and human fecal sources. Wastewater also contained clinically significant carbapenem ARGs. This study therefore provides critical insight into the distribution of ARGs in Bangladesh.

IMPORTANCE

Through the use of DNA sequencing, our study shows that there is no significant difference in the antibiotic resistance genes found in stool samples taken from individuals with high exposure to poultry routinely fed antibiotics and those without such exposure. This finding is significant as it suggests limited transmission of antibiotic resistance genes between poultry and humans in these circumstances. However, our research also demonstrates that commercially reared poultry are more likely to possess resistance genes to antibiotics commonly administered on medium-sized farms. Additionally, our study highlights the under-explored potential of wastewater as a source of various antibiotic resistance genes, some of which are clinically relevant.
Vibrio alginolyticus
growth kinetics and the metabolic effects of iron
Authors: Norfolk William A. , Shue Charlyn , Henderson W. Matthew , Glinski Donna A. , Lipp Erin K.
Published: November 2023

Vibrio alginolyticus
is a naturally occurring marine bacterium, recognized as an emerging pathogen in humans and animals and the second most common cause of vibriosis in the U.S. However, information regarding the physiology and growth of this species in the environment is limited. Here we evaluated the effects of temperature, salinity, and iron condition on the growth response across unique
V. alginolyticus
strains. A combination of growth kinetics and gas chromatography-mass spectrometry-based metabolomics studies was used to evaluate the optimal and tolerable ranges of growth and to characterize the metabolic effects of iron supplementation. All
V. alginolyticus
strains tested demonstrated broad temperature and salinity tolerance, resulting in growth at all measured temperatures (24°C–40°C) and salinities between 1% and 6% (wt/vol) NaCl with optimal growth between 30°C–36°C and 2%–4% NaCl. Environmental strains showed no growth limitation at iron concentrations ranging from 0.5- to 20.0-µM ferric Fe but demonstrated reduced growth at 0.2 µM. Likewise, the number of significantly upregulated metabolites in
V. alginolyticus
cultures grown in iron-replete (4-µM) media was greater than that in iron-deficient (~0 µM) media but varied with prior growth conditions. Detected compounds were associated with key metabolic pathways, namely, amino acid, carbohydrate, lipid, and nucleotide metabolism, suggesting that introduced iron facilitated broad activation of
V. alginolyticus
metabolism and helped to promote growth responses. Combined, these results demonstrate that
V. alginolyticus
strains are capable of rapid growth under a broad range of favorable temperature and salinity levels, which can be affected by the presence of iron.

IMPORTANCE

Transmission of
V. alginolyticus
occurs opportunistically through direct seawater exposure and is a function of its abundance in the environment. Like other
Vibrio
spp.,
V. alginolyticus
are considered conditionally rare taxa in marine waters, with populations capable of forming large, short-lived blooms under specific environmental conditions, which remain poorly defined. Prior research has established the importance of temperature and salinity as the major determinants of
Vibrio
geographical and temporal range. However, bloom formation can be strongly influenced by other factors that may be more episodic and localized, such as changes in iron availability. Here we confirm the broad temperature and salinity tolerance of
V. alginolyticus
and demonstrate the importance of iron supplementation as a key factor for growth in the absence of thermal or osmotic stress. The results of this research highlight the importance of episodic iron input as a crucial metric to consider for the assessment of
V. alginolyticus
risk.
Mapping bark bacteria: initial insights of stemflow-induced changes in bark surface phyla
Authors: Hudson J. E. , Levia D. F. , Yoshimura K. M. , Gottel N. R. , Hudson S. A. , Biddle J. F.
Published: November 2023

Life on and within bark surfaces is likely affected by many factors, including bark moisture, bark microrelief, bark pH, and the climatology of forests. The complex set of mutually interacting biotic and abiotic factors operating on bark surfaces presents a challenge in disentangling the linkages and connections between bark-dwelling organisms and biosphere-atmosphere interactions that modulate life in the canopy. Microbial communities on bark surfaces are under-represented in the literature. Given our knowledge of microbial diversity in the phyllosphere and rhizosphere and the impacts of climatology on that diversity, we hypothesized that tree bark would create a microenvironment that selects for specific microbes and that climatological and atmospheric influences from different land uses may further influence such microbial communities. Unfortunately, to our knowledge, no such study to test this hypothesis has been conducted. Recognizing this knowledge gap, samples were collected from bark and stemflow from two northern red oak trees in exurban and suburban forest fragments in the mid-Atlantic region before and after a rain event and subjected to DNA extraction and amplicon sequencing. Major phyla present on bark at both sites include Acidobacteria, Actinobacteria, Proteobacteria, and Bacteroidetes. Significant differences in amplicon sequence variants were observed between the two trees and between the northerly and southerly aspects of the sampled trees. The results of this pilot study highlight the critical need for future work examining the interplay among stemflow and microbial community composition and function (as a part of the larger ecosystem) in relation to varying land use.

IMPORTANCE

Compared with the phyllosphere, bacteria inhabiting bark surfaces are inadequately understood. Based on a preliminary pilot study, our work suggests that microbial populations vary across tree bark surfaces and may differ in relation to surrounding land use. Initial results suggest that stemflow, the water that flows along the bark surface, actively moves bacterial communities across a tree. These preliminary findings underscore the need for further study of niche microbial populations to determine whether there are connections between the biodiversity of microbiomes inhabiting corticular surfaces, land use, and hydrology.
Hepatic reactive lymphoid hyperplasia-associated primary biliary cholangitis masquerading as a neoplastic liver lesion
Authors: Sim Kwang Kiat , Fernando Tarini , Tarquinio Lorenzo , Navadgi Suresh
Published: November 2023

Hepatic reactive lymphoid hyperplasia is an uncommon benign condition, often found incidentally as a solitary liver lesion. The chronic inflammatory reaction associated with autoimmune conditions and malignancies has been postulated as a possible aetiology. The diagnosis is challenging as it often mimics various malignancies radiologically and histologically, hence the diagnosis being made only after surgical resection. Lymphadenopathy is common with primary biliary cholangitis, though rarely reported with reactive lymphoid hyperplasia. We report a case of hepatic reactive lymphoid hyperplasia associated with portacaval lymphadenopathy in a patient with primary biliary cholangitis, diagnosed after surgical resection. We propose lesional biopsy be considered in patients with primary biliary cholangitis found to have a solitary lesion with supporting low-risk clinical and radiological features.
Impact of dexmedetomidine on mortality in critically ill patients with acute kidney injury: a retrospective propensity score matching analysis
Authors: Wang Wenting , Jin Yu , Zhang Peiyao , Gao Peng , Wang He , Liu Jinping
Published: November 2023

Objectives

This study sought to estimate the effect of dexmedetomidine (DEX) administration on mortality in critically ill patients with acute kidney injury (AKI).

Design

A retrospective cohort study.

Setting

The study sourced its data from the Multiparameter Intelligent Monitoring in Intensive Care Database IV (MIMIC-IV), a comprehensive database of intensive care unit patients.

Participants

A total of 15 754 critically ill patients with AKI were enrolled from the MIMIC-IV database.

Primary and secondary outcome

Primary outcome was in-hospital mortality and secondary outcome was 180-day mortality.

Results

15 754 critically ill AKI patients were included in our analysis. We found that DEX use decreased in-hospital mortality risk by 38% (HR 0.62, 95% CI 0.55 to 0.70) and 180-day mortality risk by 23% (HR 0.77, 95% CI 0.69 to 0.85). After adjusting for confounding factors, DEX can reduce all three stages of AKI in in-hospital mortality.

Conclusions

Our retrospective cohort study suggests that DEX significantly correlates with decreased risk-adjusted in-hospital and 180-day mortality in critically ill AKI patients. Nonetheless, future randomised controlled trials are warranted to validate our findings.