bluuebunny/crossref_metadata_2025 huggingface dataset:
From the Interpretation of Quantum Mechanics to Quantum Technologies
Authors: Freire Junior Olival
Published: May 2024

Quantum mechanics emerged laden with issues and doubts about its foundations and interpretation. However, nobody in the 1920s and 1930s dared to conjecture that research on such issues would open the doors to developments so huge as to require the term second quantum revolution to describe them. On the one hand, the new theory saw its scope of applications widen in various domains including atoms, molecules, light, the interaction between light and matter, relativistic effects, field quantization, nuclear physics, and solid state and particle physics. On the other hand, there were debates on alternative interpretations, the status of statistical predictions, the completeness of the theory, the underlying logic, mathematical structures, the understanding of measurements, and the transition from the quantum to the classical description. Until the early 1960s, there seemed to be a coexistence between these two orders of issues, without any interaction between them.

From the late 1960s on, however, this landscape underwent dramatic changes. The main factor of change was Bell’s theorem, which implied a conflict between quantum mechanics predictions for certain systems that are spatially separated and the assumption of local realism. Experimental tests of this theorem led to the corroboration of quantum predictions and the understanding of quantum entanglement as a physical feature, a result that justified the 2022 Nobel Prize. Another theoretical breakthrough was the understanding and calculation of the interaction of a quantum system with its environment, leading to the transition from pure to mixed states, a feature now known as decoherence. Entanglement and decoherence both resulted from the dialogue between research on the foundations and quantum predictions. In addition, research on quantum optics and quantum gravity benefitted debates on the foundations. From the early 1980s on, another major change occurred, now in terms of experimental techniques, allowing physicists to manipulate single quantum systems and taking the thought experiments of the founders of quantum mechanics into the labs. Lastly, the insight that quantum systems may be used in computing opened the doors to the first quantum algorithms. Altogether, these developments have produced a new field of research, quantum information, which has quantum computers as its holy grail. The term second quantum revolution distinguishes these new achievements from the first spin-offs of quantum mechanics, for example, transistors, electronic microscopes, magnetic resonance imaging, and lasers. Nowadays the applications of this second revolution have gone beyond computing to include sensors and metrology, for instance, and thus are better labeled as quantum technologies.
The Role of National Academies and Scientific Societies in Public Policy
Authors: Hardaker Paul
Published: May 2024

Public policy is collectively the way in which governments the world over seek to address issues, solve problems, or take actions that move society forward. It is a dynamic, complex, and interactive process with many actors. National academies and scientific societies play a crucial role within this space as an independent and trusted voice, collating and representing the evidence base and setting out areas of priority for governments to focus on. They do this not only by marshaling expert advice and thought from within their own disciplines and areas but also by bringing together coalitions, partnerships, and advocacy groups, to amplify their voices and to help them engage with governments in a more focused and coherent way. This helps not only to inform and influence public policy but also to hold governments to account in areas of public interest. Increasingly, societies are taking on greater advocacy roles and campaigning on key issues and this has brought more emphasis to bear on their skillsets, working with new and different partners in the policy space, and the role of open science and greater public engagement going forward.
Grief, Sadness, and Depression in the Hebrew Bible and Ancient Near East
Authors: Bosworth David A.
Published: May 2024

Experiences of loss (of person, property, health, security, etc.) trigger grief. The experience of grief is universal, and some expressions of sorrow likewise appear across the human species (e.g., weeping). Attachment theory has described fundamental aspects of grief that appear in all human cultures and many animal species. It is a well-established, empirically grounded theory that enables one to recognize and analyze grief in ancient texts. Universal aspects of grief appear refracted through the lens of particular cultures. Some grief-motivated behaviors appear entirely culturally conditioned, while others are strongly influenced by biology. For example, ancient Israelite people tore their garments and placed dust on themselves as an expression of grief, but modern Western people do not. Israelites also wept and moaned, and these behaviors can be seen across time and place. Weeping is a shared human inheritance that arose in the evolution of the species. Humans also evolved the capacity for culture, which shapes weeping and other emotional expressions. Some cultures expect mourners to minimize public displays of grief, while others expect loud moaning and copious tears in public displays of grief, sometimes led by professional mourners.
Shari’a Tribunals in North America
Authors: Richardson James T. , Turner Bryan S.
Published: May 2024

Some North American societies, especially Canada and the United States, are experiencing increasing numbers of Muslim citizens, and those communities have grown and become more integrated into the two societies. Predictably, they have sought the right to practice their faith in ways similar to how other minority religions are treated within the relatively open societies in which they reside. However, tragic events such as the destruction of the World Trade Center has led to considerable animus toward Muslims within the two societies, thus impeding efforts to seek more acceptance of Islamic practices, such as when settling domestic disputes involving divorce, child custody, and inheritance. Controversies have erupted in both the United States and Canada over efforts to allow arbitration in the area of domestic affairs for Muslims. A number of scholars have addressed this topic, often using previously accepted treatments of Jewish minorities as a model. The pros and cons of such an approach have been presented, leading to the conclusion from many of those scholars that allowing, within certain limits, recognition of Muslim practices within the domestic relations area would be beneficial both to the societies at large and to the Muslim citizens residing within them.
Pragmatic Approaches to Germanic Languages
Authors: Aijmer Karin
Published: May 2024

Elements that have pragmatic functions are, for example, pragmatic markers, modal particles, vocatives, conversational routines (apologies, thanks), interjections, pauses, tag questions, general extenders, response forms, and comment clauses.

Pragmatic markers are frequent in English and other Germanic languages. They can be analyzed based on a form-to-function approach drawing on different theoretical frameworks such as conversation analysis, interactional linguistics, or relevance theory. A pervasive change in the orientation of pragmatics has been achieved by its broadening to the study of variation. Pragmatic markers have, for example, been compared across languages regarding their position in the sentence and combinability with other pragmatic markers. Another “red thread” in the development of pragmatics in Germanic languages is the availability of spoken corpora facilitating the empirical analysis of the relationship between form, function, and context. Modal particles, interjections, and hesitation markers are regarded as subclasses of pragmatic markers that can be given a functional analysis. Modal particles are studied especially in German, where they are generally regarded as a special word class distinct from pragmatic markers. Address forms may vary across languages and varieties of languages depending on social factors and cultural preferences. Many Germanic languages (but not English) make a distinction between the informal T-pronoun of address in the singular (Swedish du; German du) and a formal plural V-form of address (Swedish ni; German sie). Politeness and speech acts are another central research area in pragmatics. Some researchers have applied a conversation analysis approach to the study of speech acts such as requests and compliments. The majority of speech act studies are based on discourse completion tests and role-plays. Corpora are less suited to analyze speech acts unless the forms are routinized. One way to solve this methodological problem is indicated by the development of schemes for pragmatically annotating speech acts in corpora.
Alignment and Word Order in the Romance Languages
Authors: Rovai Francesco
Published: May 2024

The term “alignment” refers to the formal realization of the argument structure of the clause, that is, the ways in which the core arguments of the predicate are encoded by means of three main morphosyntactic devices: nominal case marking (morphological case, adpositions), verb marking systems (verbal agreement, pronominal affixes, auxiliaries, voice distinctions, etc.), and word order. The relative importance of these mechanisms of argument coding may considerably vary from language to language. In the Romance family, a major role is played by finite verb agreement and, to a lesser extent, auxiliary selection, participial agreement, voice distinctions, and word order, depending on the language/variety. Most typically, both transitive and intransitive subjects share the same formal coding (they control finite verb agreement and precede the verb in the basic word order) and are distinguished from direct objects (which do not control finite verb agreement and follow the verb in the basic word order). This arrangement of the argument structure is traditionally known as “nominative/accusative” alignment and can be easily identified as the main alignment of the Romance languages. Note that, with very few exceptions, nominal case marking is instead “neutral,” since no overt morphological distinction is made between subject and object arguments after the loss of the Latin case system.

However, although the Romance languages can legitimately be associated with an accusative alignment, it must be borne in mind that, whatever the property selected, natural languages speak against an all-encompassing, holistic typology. A language “belongs” to an alignment type only insofar as it displays a significantly above-average frequency of clause structures with that kind of argument coding, but this does not exclude the existence of several grammatical domains that partake of different alignments. In the Romance family, minor patterns are attested that are not consistent with an accusative alignment. In part, they depend on robust crosslinguistic tendencies in the distribution of the different alignment types when they coexist in the same language. In part, they reflect phenomena of morphosyntactic realignment that can be traced back to the transition from Latin to Romance, when, alongside the dominant accusative alignment of the classical language, Late Latin developed an active alignment in some domains of the grammar—a development that has its roots in Classical and Early Latin. Today, the Romance languages preserve traces of this intermediate stage, but in large part, the signs of it have been replaced with novel accusative structures. In particular, at the level of the sentence, there emerges an accusative-aligned word order, with the preverbal position realizing the default “subject” position and the postverbal position instantiating the default “object” position.
Assessing Gender Leadership and the Cultural Aspect of Disaster Response in Developing Context Focusing on the Case of the Beirut Explosion
Authors: Nasser Fatima , Haddad Tania , Mezher Hala
Published: May 2024

Disaster risk reduction (DRR) addresses social equity, environmental protection, and economic growth risks. It is defined as the conceptual framework that involves carefully examined elements for their potential to reduce vulnerabilities and mitigate disaster risks across a society. The primary goals are to prevent or, alternatively, to minimize the adverse impacts of hazards through mitigation and preparedness measures, all within the overarching context of promoting sustainable development. DRR should be a significant component of policies and development strategies for governments since it minimizes vulnerabilities; hence, it is important to build a culture of prevention to identify daily hazards and reduce the effects of disasters.

Due to gender inequalities, women are disproportionately affected by disasters, as they are more vulnerable to losing their livelihoods and houses, gender-based violence, and loss of life pre- and post-disaster. Disaster response and risk reduction policies and practices often replicate existing social structures that sideline and de-prioritize marginalized groups. However, women are showing their capability to respond to and recover from crises by building community resilience and participating in DRR at the forefront of the recovery response. Women contribute firsthand insights and solutions, possessing a nuanced understanding of their vulnerabilities and recognizing disasters’ distinct impact on both women and girls.

This is evident as women within a patriarchal system actively assumed leadership roles, challenging the established norms. Their engagement reflects a steadfast commitment to promoting a more equitable approach to disaster response.

There is a lack of empirical research that indicates how gender leadership can lead to risk disaster reduction and social changes in Lebanon. In order to expand the existing literature on women’s leadership in disaster management and to ascertain the substantial contribution of women in fostering resilience for DRR, thereby instigating societal change in developing contexts, there is a need to tackle two core inquiries:

What is the role of women’s leadership in disaster management in Lebanon?

How does women’s leadership lead to DRR and social changes in the context of disasters in developing countries?
Ecosystem Benefits of Large Dead Wood in Freshwater Environments
Authors: Wohl Ellen
Published: May 2024

Large wood in freshwater environments is downed, dead wood pieces in river channels, floodplains, wetlands, and lakes. Large wood was historically much more abundant in freshwaters, but decades to centuries of deforestation and direct wood removal have decreased wood loads—volumes of large wood per unit area—in freshwaters around the world. The widespread public perception that large wood is undesirable in freshwater environments contrasts with scientific understanding of the beneficial effects of large wood. Large wood tends to increase the spatial heterogeneity of hydraulics, substrate, channel planform, and the floodplain and hyporheic zone in rivers. This equates to greater habitat diversity and refugia for organisms, as well as energy dissipation and storage of materials during floods, which can increase the resilience of the river to disturbances such as wildfire, drought, and flooding. Similarly, wood in lakes increases lakeshore and lakebed heterogeneity of hydraulics, substrate, habitat, nutrient uptake, and storage of particulate organic matter and sediment. Large wood in rivers and lakes provides an array of vital ecosystem functions, and both individual species and biotic communities are adversely affected by a lack of wood in rivers and lakes that have been managed in a way that reduces wood loads. River and lake management are now more likely to include protection of existing large wood and active reintroduction of large wood, but numerous questions remain regarding appropriate targets for wood loads in different environmental settings, including potential threshold wood loads necessary to create desired effects. Large wood can also directly and indirectly enhance carbon storage in freshwater environments, but this storage remains poorly quantified.
Error modelled gene expression analysis (EMOGEA) provides a superior overview of time course RNA-seq measurements and low count gene expression
Authors: Barra Jasmine , Taverna Federico , Bong Fabian , Ahmed Ibrahim , Karakach Tobias K
Published: May 2024

Temporal RNA-sequencing (RNA-seq) studies of bulk samples provide an opportunity for improved understanding of gene regulation during dynamic phenomena such as development, tumor progression or response to an incremental dose of a pharmacotherapeutic. Moreover, single-cell RNA-seq (scRNA-seq) data implicitly exhibit temporal characteristics because gene expression values recapitulate dynamic processes such as cellular transitions. Unfortunately, temporal RNA-seq data continue to be analyzed by methods that ignore this ordinal structure and yield results that are often difficult to interpret. Here, we present Error Modelled Gene Expression Analysis (EMOGEA), a framework for analyzing RNA-seq data that incorporates measurement uncertainty, while introducing a special formulation for those acquired to monitor dynamic phenomena. This method is specifically suited for RNA-seq studies in which low-count transcripts with small-fold changes lead to significant biological effects. Such transcripts include genes involved in signaling and non-coding RNAs that inherently exhibit low levels of expression. Using simulation studies, we show that this framework down-weights samples that exhibit extreme responses such as batch effects allowing them to be modeled with the rest of the samples and maintain the degrees of freedom originally envisioned for a study. Using temporal experimental data, we demonstrate the framework by extracting a cascade of gene expression waves from a well-designed RNA-seq study of zebrafish embryogenesis and an scRNA-seq study of mouse pre-implantation and provide unique biological insights into the regulation of genes in each wave. For non-ordinal measurements, we show that EMOGEA has a much higher rate of true positive calls and a vanishingly small rate of false negative discoveries compared to common approaches. Finally, we provide two packages in Python and R that are self-contained and easy to use, including test data.
A perspective on genetic and polygenic risk scores—advances and limitations and overview of associated tools
Authors: Schwarzerova Jana , Hurta Martin , Barton Vojtech , Lexa Matej , Walther Dirk , Provaznik Valentine , Weckwerth Wolfram
Published: May 2024

Polygenetic Risk Scores are used to evaluate an individual's vulnerability to developing specific diseases or conditions based on their genetic composition, by taking into account numerous genetic variations. This article provides an overview of the concept of Polygenic Risk Scores (PRS). We elucidate the historical advancements of PRS, their advantages and shortcomings in comparison with other predictive methods, and discuss their conceptual limitations in light of the complexity of biological systems. Furthermore, we provide a survey of published tools for computing PRS and associated resources. The various tools and software packages are categorized based on their technical utility for users or prospective developers. Understanding the array of available tools and their limitations is crucial for accurately assessing and predicting disease risks, facilitating early interventions, and guiding personalized healthcare decisions. Additionally, we also identify potential new avenues for future bioinformatic analyzes and advancements related to PRS.
Integrating Reinforcement Learning and Monte Carlo Tree Search for enhanced neoantigen vaccine design
Authors: Lin Yicheng , Ma Jiakang , Yuan Haozhe , Chen Ziqiang , Xu Xingyu , Jiang Mengping , Zhu Jialiang , Meng Weida , Qiu Wenqing , Liu Yun
Published: May 2024

Recent advances in cancer immunotherapy have highlighted the potential of neoantigen-based vaccines. However, the design of such vaccines is hindered by the possibility of weak binding affinity between the peptides and the patient’s specific human leukocyte antigen (HLA) alleles, which may not elicit a robust adaptive immune response. Triggering cross-immunity by utilizing peptide mutations that have enhanced binding affinity to target HLA molecules, while preserving their homology with the original one, can be a promising avenue for neoantigen vaccine design. In this study, we introduced UltraMutate, a novel algorithm that combines Reinforcement Learning and Monte Carlo Tree Search, which identifies peptide mutations that not only exhibit enhanced binding affinities to target HLA molecules but also retains a high degree of homology with the original neoantigen. UltraMutate outperformed existing state-of-the-art methods in identifying affinity-enhancing mutations in an independent test set consisting of 3660 peptide–HLA pairs. UltraMutate further showed its applicability in the design of peptide vaccines for Human Papillomavirus and Human Cytomegalovirus, demonstrating its potential as a promising tool in the advancement of personalized immunotherapy.
Volumetric and diffusion MRI abnormalities associated with dysarthria in multiple sclerosis
Authors: Kenyon Katherine H , Strik Myrte , Noffs Gustavo , Morgan Angela , Kolbe Scott , Harding Ian H , Vogel Adam P , Boonstra Frederique M C , van der Walt Anneke
Published: May 2024

Up to half of all people with multiple sclerosis experience communication difficulties due to dysarthria, a disorder that impacts the motor aspects of speech production. Dysarthria in multiple sclerosis is linked to cerebellar dysfunction, disease severity and lesion load, but the neuroanatomical substrates of these symptoms remain unclear. In this study, 52 participants with multiple sclerosis and 14 age- and sex-matched healthy controls underwent structural and diffusion MRI, clinical assessment of disease severity and cerebellar dysfunction and a battery of motor speech tasks. Assessments of regional brain volume and white matter integrity, and their relationships with clinical and speech measures, were undertaken. White matter tracts of interest included the interhemispheric sensorimotor tract, cerebello-thalamo-cortical tract and arcuate fasciculus, based on their roles in motor and speech behaviours. Volumetric analyses were targeted to Broca’s area, Wernicke’s area, the corpus callosum, thalamus and cerebellum. Our results indicated that multiple sclerosis participants scored worse on all motor speech tasks. Fixel-based diffusion MRI analyses showed significant evidence of white matter tract atrophy in each tract of interest. Correlational analyses further indicated that higher speech naturalness—a perceptual measure of dysarthria—and lower reading rate were associated with axonal damage in the interhemispheric sensorimotor tract and left arcuate fasciculus in people with multiple sclerosis. Axonal damage in all tracts of interest also correlated with clinical scales sensitive to cerebellar dysfunction. Participants with multiple sclerosis had lower volumes of the thalamus and corpus callosum compared with controls, although no brain volumetrics correlated with measures of dysarthria. These findings indicate that axonal damage, particularly when measured using diffusion metrics, underpin dysarthria in multiple sclerosis.
Single-molecule characterization of salivary protein aggregates from Parkinson’s disease patients: a pilot study
Authors: Furlepa Martin , Zhang Yu P , Lobanova Evgeniia , Kahanawita Lakmini , Vivacqua Giorgio , Williams-Gray Caroline H , Klenerman David
Published: May 2024

Saliva is a convenient and accessible biofluid that has potential as a future diagnostic tool for Parkinson’s disease. Candidate diagnostic tests for Parkinson’s disease to date have predominantly focused on measurements of α-synuclein in CSF, but there is a need for accurate tests utilizing more easily accessible sample types. Prior studies utilizing saliva have used bulk measurements of salivary α-synuclein to provide diagnostic insight. Aggregate structure may influence the contribution of α-synuclein to disease pathology. Single-molecule approaches can characterize the structure of individual aggregates present in the biofluid and may, therefore, provide greater insight than bulk measurements. We have employed an antibody-based single-molecule pulldown assay to quantify salivary α-synuclein and amyloid-β peptide aggregate numbers and subsequently super-resolved captured aggregates using direct Stochastic Optical Reconstruction Microscopy to describe their morphological features. We show that the salivary α-synuclein aggregate/amyloid-β aggregate ratio is increased almost 2-fold in patients with Parkinson’s disease (n = 20) compared with controls (n = 20, P < 0.05). Morphological information also provides insight, with saliva from patients with Parkinson’s disease containing a greater proportion of larger and more fibrillar amyloid-β aggregates than control saliva (P < 0.05). Furthermore, the combination of count and morphology data provides greater diagnostic value than either measure alone, distinguishing between patients with Parkinson’s disease (n = 17) and controls (n = 18) with a high degree of accuracy (area under the curve = 0.87, P < 0.001) and a larger dynamic range. We, therefore, demonstrate for the first time the application of highly sensitive single-molecule imaging techniques to saliva. In addition, we show that aggregates present within saliva retain relevant structural information, further expanding the potential utility of saliva-based diagnostic methods.
Megalin Knockout Reduces SGLT2 Expression and Sensitizes to Western Diet-induced Kidney Injury
Authors: Youm Elynna B , Shipman Katherine E , Albalawy Wafaa N , Vandevender Amber M , Sipula Ian J , Rbaibi Youssef , Marciszyn Allison E , Lashway Jared A , Brown Emma E , Bondi Corry B , Boyd-Shiwarski Cary R , Tan Roderick J , Jurczak Michael J , Weisz Ora A
Published: May 2024

Megalin (Lrp2) is a multiligand receptor that drives endocytic flux in the kidney proximal tubule (PT) and is necessary for the recovery of albumin and other filtered proteins that escape the glomerular filtration barrier. Studies in our lab have shown that knockout (KO) of Lrp2 in opossum PT cells leads to a dramatic reduction in sodium–glucose co-transporter 2 (SGLT2) transcript and protein levels, as well as differential expression of genes involved in mitochondrial and metabolic function. SGLT2 transcript levels are reduced more modestly in Lrp2 KO mice. Here, we investigated the effects of Lrp2 KO on kidney function and health in mice fed regular chow (RC) or a Western-style diet (WD) high in fat and refined sugar. Despite a modest reduction in SGLT2 expression, Lrp2 KO mice on either diet showed increased glucose tolerance compared to control mice. Moreover, Lrp2 KO mice were protected against WD-induced fat gain. Surprisingly, renal function in male Lrp2 KO mice on WD was compromised, and the mice exhibited significant kidney injury compared with control mice on WD. Female Lrp2 KO mice were less susceptible to WD-induced kidney injury than male Lrp2 KO. Together, our findings reveal both positive and negative contributions of megalin expression to metabolic health, and highlight a megalin-mediated sex-dependent response to injury following WD.
Copy number and sequence variation in rDNA of Daphnia pulex from natural populations: insights from whole-genome sequencing
Authors: Elguweidi Abir , Crease Teresa
Published: May 2024

Ribosomal DNA (rDNA) has a vital role in ribosome biogenesis as it contains the genes that encode ribosomal RNA (rRNA) separated by intergenic spacers (IGSs). The rRNA genes occur in hundreds to tens of thousands of copies per haploid genome in eukaryotes and are generally highly conserved with low variation within species. Due to the repetitive nature and large size of rDNA arrays, detecting intraindividual variation can be difficult. In this study, we use whole-genome sequences of 169 Daphnia pulex individuals from 10 natural populations to measure the copy number and sequence variation in rDNA. This revealed that variation in rDNA copy number between individuals spans an order of magnitude. We further observed a substantial level of sequence variation within individual genomes. As expected, single-nucleotide polymorphisms occurred in regions of lower functional constraint such as the IGS and expansion segments of the rRNA genes. The presence of strong linkage disequilibrium among variants facilitated identification of haplotypes within each population. Although there was evidence of recombination among haplotypes from different populations, it is insufficient to eliminate linkage disequilibrium within populations. Estimating copy number and haplotype diversity within individuals revealed that the level of intraindividual sequence variation is not strongly correlated with copy number. The observed patterns of variation highlight a complex evolutionary history of rDNA in D. pulex. Future research should explore the functional implications of rDNA copy number and sequence variation on organismal phenotypes.
Paw-Sitive Reception for Robot Guide Dog
Authors: Cooper Martin
Published: May 2024

Working in partnership with charities, AI and robotics experts from the University of Glasgow have demonstrated a robotic guide dog designed to help partially sighted people navigate indoor spaces.
Disrupted one-carbon metabolism in heifers negatively affects their health and physiology
Authors: Crouse Matthew S , Trotta Ronald J , Freetly Harvey C , Lindholm-Perry Amanda K , Neville Bryan W , Oliver William T , Hammer Carrie J , Syring Jessica G , King Layla E , Neville Tammi L , Reynolds Lawrence P , Dahlen Carl R , Caton Joel S , Ward Alison K , Cushman Robert A
Published: May 2024

The objective of this study was to determine the dose-dependent response of one-carbon metabolite (OCM: methionine, choline, folate, and vitamin B12) supplementation on heifer dry matter intake on fixed gain, organ mass, hematology, cytokine concentration, pancreatic and jejunal enzyme activity, and muscle hydrogen peroxide production. Angus heifers (n = 30; body weight [BW] = 392.6 ± 12.6 kg) were individually fed and assigned to one of five treatments: 0XNEG: total mixed ration (TMR) and saline injections at days 0 and 7 of the estrous cycle, 0XPOS: TMR, rumen-protected methionine (MET) fed at 0.08% of the diet dry matter, rumen-protected choline (CHOL) fed at 60 g/d, and saline injections at days 0 and 7, 0.5X: TMR, MET, CHOL, 5-mg B12, and 80-mg folate injections at days 0 and 7, 1X: TMR, MET CHOL, 10-mg vitamin B12, and 160-mg folate at days 0 and 7, and 2X: TMR, MET, CHOL, 20-mg vitamin B12, and 320-mg folate at days 0 and 7. All heifers were estrus synchronized but not bred, and blood samples were collected on days 0, 7, and at slaughter (day 14) during which tissues were collected. By design, heifer ADG did not differ (P = 0.96). Spleen weight and uterine weight were affected cubically (P = 0.03) decreasing from 0XPOS to 0.5X. Ovarian weight decreased linearly (P < 0.01) with increasing folate and B12 injection. Hemoglobin and hematocrit percentage were decreased (P < 0.01) in the 0.5X treatment compared with all other treatments. Plasma glucose, histotroph protein, and pancreatic α-amylase were decreased (P ≤ 0.04) in the 0.5X treatment. Heifers on the 2X treatment had greater pancreatic α-amylase compared with 0XNEG and 0.5X treatment. Interleukin-6 in plasma tended (P = 0.08) to be greater in the 0XPOS heifers compared with all other treatments. Lastly, 0XPOS-treated heifers had reduced (P ≤ 0.07) hydrogen peroxide production in muscle compared with 0XNEG heifers. These data imply that while certain doses of OCM do not improve whole animal physiology, OCM supplementation doses that disrupt one-carbon metabolism, such as that of the 0.5X treatment, can induce a negative systemic response that results in negative effects in both the dam and the conceptus during early gestation. Therefore, it is necessary to simultaneously establish an optimal OCM dose that increases circulating concentrations for use by the dam and the conceptus, while avoiding potential negative side effects of a disruptive OCM, to evaluate the long-term impacts of OCM supplementation of offspring programming.
A review of the varunid crab genusParapyxidognathusWard, 1941 (Decapoda: Brachyura: Varunidae), with descriptions of two new species
Authors: Hsu Jhih-Wei , Shih Hsi-Te
Published: May 2024

Species of Parapyxidognathus Ward, 1941 are distributed across tropical Indo-West Pacific to temperate downstream rivers and in estuaries. The genus previously included only one species, Parapyxidognathus deianira (De Man, 1888). We examined specimens from Parapyxidognathus and its closely related genus, Pyxidognathus A. Milne-Edwards, 1879 from the eastern Indian Ocean and western Pacific, focusing on their morphological characters. The results also support the reclassification of Pyxidognathus fluviatilis Alcock, 1900 into Parapyxidognathus, as well as the establishment of two new species from the western Pacific, Pa. tshiansuesp. nov. and Pa. ongiasp. nov. The identity of the species is supported by evidence from mitochondrial 16S rDNA and cytochrome oxidase subunit 1 (COI) genes. There are now four species in Parapyxidognathus distinguishable by the characters of the anterolateral teeth of the carapace, the pleon, and the first gonopods of the male, and the female vulvae.
An unusual case of an extensive post-injection retroperitoneal abscess in an intravenous drug user
Authors: Gerasopoulos Georgios , Patriarcheas Vasileios , Mitsas Angelos C , Karagianni Foteini , Routis Panagiotis , Kostis Minas , Voultsinos Vasileios , Lazaridis Michail , Tsitlakidis Anastasios
Published: May 2024

Retroperitoneal abscesses constitute an uncommon, complex, and life-threatening intra-abdominal infection. The insidious nature of the presentation, coupled with the presence of non-specific clinical symptoms, might result in misdiagnosis or delayed diagnosis, ultimately contributing to substantial morbidity and mortality. Herein we report a case of a 32-year-old intravenous drug user who presented to the emergency department complaining of high-grade fever, intense hiccough, and back pain due to retroperitoneal abscess formation after intravenous injection in the left femoral vein.
Escherichia coli non-coding regulatory regions are highly conserved
Authors: Lamoureux Cameron R , Phaneuf Patrick V , Palsson Bernhard O , Zielinski Daniel C
Published: May 2024

Microbial genome sequences are rapidly accumulating, enabling large-scale studies of sequence variation. Existing studies primarily focus on coding regions to study amino acid substitution patterns in proteins. However, non-coding regulatory regions also play a distinct role in determining physiologic responses. To investigate intergenic sequence variation on a large-scale, we identified non-coding regulatory region alleles across 2350 Escherichia coli strains. This ‘alleleome’ consists of 117 781 unique alleles for 1169 reference regulatory regions (transcribing 1975 genes) at single base-pair resolution. We find that 64% of nucleotide positions are invariant, and variant positions vary in a median of just 0.6% of strains. Additionally, non-coding alleles are sufficient to recover E. coli phylogroups. We find that core promoter elements and transcription factor binding sites are significantly conserved, especially those located upstream of essential or highly-expressed genes. However, variability in conservation of transcription factor binding sites is significant both within and across regulons. Finally, we contrast mutations acquired during adaptive laboratory evolution with wild-type variation, finding that the former preferentially alter positions that the latter conserves. Overall, this analysis elucidates the wealth of information found in E. coli non-coding sequence variation and expands pangenomic studies to non-coding regulatory regions at single-nucleotide resolution.
Hermeneutical disarmament
Authors: Morgan Robert
Published: May 2024

When words and phrases change their meaning, we might find ourselves less able to understand and communicate, and this can be harmful to us. I make sense of this by introducing the concept of hermeneutical disarmament. Hermeneutical disarmament is the process by which a person is rendered less able to understand or communicate experiences, ideas, and other phenomena as a result of semantic change to the linguistic resources that could previously have been deployed for these purposes. I defend this concept by showing that semantic change can inflict cognitive and communicative harms and detail some of the forms that it can take.
Does long-term drought or repeated defoliation affect seasonal leaf N cycling in young beech trees?
Authors: Massonnet Catherine , Chuste Pierre-Antoine , Zeller Bernhard , Tillard Pascal , Gerard Bastien , Cheraft Loucif , Breda Nathalie , Maillard Pascale
Published: May 2024

Forest trees adopt effective strategies to optimize nitrogen (N) use through internal N recycling. In the context of more recurrent environmental stresses due to climate change, the question remains of whether increased frequency of drought or defoliation threatens this internal N recycling strategy. We submitted 8-year-old beech trees to 2 years of either severe drought (Dro) or manual defoliation (Def) to create a state of N starvation. At the end of the second year before leaf senescence, we labeled the foliage of the Dro and Def trees, as well as that of control (Co) trees, with 15N-urea. Leaf N resorption, winter tree N storage (total N, 15N, amino acids, soluble proteins) and N remobilization in spring were evaluated for the three treatments. Defoliation and drought did not significantly impact foliar N resorption or N concentrations in organs in winter. Total N amounts in Def tree remained close to those in Co tree, but winter N was stored more in the branches than in the trunk and roots. Total N amount in Dro trees was drastically reduced (−55%), especially at the trunk level, but soluble protein concentrations increased in the trunk and fine roots compared with Co trees. During spring, 15N was mobilized from the trunk, branches and twigs of both Co and Def trees to support leaf growth. It was only provided through twig 15N remobilization in the Dro trees, thus resulting in extremely reduced Dro leaf N amounts. Our results suggest that stress-induced changes occur in N metabolism but with varying severity depending on the constraints: within-tree 15N transport and storage strategy changed in response to defoliation, whereas a soil water deficit induced a drastic reduction of the N amounts in all the tree organs. Consequently, N dysfunction could be involved in drought-induced beech tree mortality under the future climate.
Foliar Inoculation of Phyllachora maydis into Corn Induces Infection and Local Spread in Field Environments
Authors: Solórzano José E. , Subbaiah Aarav , Floyd Crystal M. , Kleczewski Nathan M. , Malvick Dean K.
Published: May 2024

Tar spot of corn (Zea mays L.) is a significant disease in the United States and Canada caused by Phyllachora maydis, an obligate biotroph fungus. However, field research critical for understanding and managing the disease has been hindered by a need for methods to inoculate corn with P. maydis in field environments. In this study, we developed and demonstrated the efficacy of a method to initiate tar spot in field settings using inoculations of corn leaves with P. maydis inoculum that had been stored at −20°C for 10 months. Stromata of P. maydis were observed 19 days after inoculations in two field experiments, and stromata resulting from secondary spread were initially observed 39 to 41 days after the initial inoculations. Tar spot was not present in the fields beyond the inoculated areas or localized spread area, signifying that the establishment of initial disease resulted solely from inoculations. This study enhances our understanding of inoculation and infection of corn with P. maydis and tar spot development in field environments. The results will aid new research into understanding the corn tar spot pathosystem and improving management strategies.
Meta-Analysis in Plant Pathology: Publication Patterns, Methodological Trends, and Potential Future Directions
Authors: Del Ponte Emerson M. , Barro Jhonatan P. , Madden Laurence V.
Published: May 2024

Meta-analysis (MA) is increasingly adopted in agricultural and ecological sciences, fields at the interface with plant pathology. Our review of the use of MA in the field since 1999 identified 79 original research papers. Fifty percent of these works were published in two American Phytopathological Society journals, emphasizing their central role in disseminating MA research. Analysis of the number of authors per study and the authorship network revealed a tightly knit field. The network shows a few “hub” authors or groups that significantly influence research directions, with a clear geographical clustering in North and South America. Most of the MA papers focused on the effects of disease control, where fungicide was the main product. The MA investigations often focus on response variables like yield and disease severity for which the analyzed effect sizes differ, but the log of the ratio of means and untransformed means are predominant. The study selection to be included in the MA often follows systematic review standards or when clear quantitative criteria are used for study inclusion. Yet, the inclusion of data from reports, newsletters, and research trials adds breadth. Frequentist rather than Bayesian inference is most common, and SAS and R are the preferred software. Our review underscores the escalating importance of MA in plant pathology, especially for determining the mean and variability of the effects of different control methods on disease and yield. Efforts should continue to improve the detailed reporting of MA methods used, data sharing, and reporting of measures of heterogeneity among studies.
High-Quality Complete Genome Sequence of Xanthomonas phaseoli pv. dieffenbachiae Outbreak Strain D182: The Causative Agent of Anthurium Bacterial Blight in Hawaii
Authors: Dobhal Shefali , Chuang Shu-Cheng , Arizala Dario , Keith Lisa M. , Alvarez Anne M. , Arif Mohammad
Published: May 2024

Xanthomonas phaseoli pv. dieffenbachiae (Xpd), the causal agent of anthurium blight, is classified as an A2 quarantine organism on the European and Mediterranean Plant Protection Organization (EPPO) list due to its devastating impact on the anthurium industry. In this study, we sequenced strain D182, representative of the Hawaiian anthurium blight outbreak (1981 to 1986), using PacBio RS II SMRT technology. High-quality de novo assembly of 5,217,888 bp (65% GC) was generated with a mean coverage of 351× using HGAP v4. Strain D182 harbors one plasmid (73.5 kb, 60.8% GC). Average nucleotide identity and digital DNA–DNA hybridization values of 99.86 and 98.9%, respectively, showed close phylogenetic relationships with Xpd strain LMG 695PT. The genome information will be useful in providing insights into the genomic biology, virulence mechanisms, and evolutionary relationships of Xpd and other strains associated with anthurium blight outbreaks worldwide.

[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Elbow Flexor Release Combined With Selective Neurectomy of Musculocutaneous Nerve for Spastic Elbow Flexion Deformity in Children and Adolescents
Authors: De Lepeleere Bram , Fitoussi Frank
Published: May 2024

Background:

Spasticity of the elbow flexors causes a dynamic and/or static elbow flexion deformity. This position interferes with the functional use of the hand, is aesthetically unpleasant and can cause problems with hygiene and comfort. A lengthening procedure of elbow flexor muscles can improve elbow posture and range of motion. However, causal spasticity is not addressed directly. Selective neurectomy of the musculocutaneous nerve has a direct effect on underlying spasticity but is not sufficient when contracture is present. In this study, we examine the long-term results of a combined surgical approach: a release procedure of the elbow flexors and selective neurectomy of the musculocutaneous nerve.

Methods:

A retrospective study of 14 patients with spastic flexion deformity of the elbow was performed. After a mean follow-up of 52.6 months (SD 33, range 12 to 113), the results of the combined surgical approach were evaluated. Spontaneous position of the elbow and active and passive range of motion were assesses using goniometry. Spasticity was assessed using the Modified Ashworth Scale. Function of the affected upper limb before and after surgery was assessed by the House functional classification. Patient and caretaker’s satisfaction were assessed using a visual analogue scale.

Results:

The mean decrease of passive elbow extension deficit was 34 degrees (SD 21.3, P<0.05). Active elbow extension increased with a mean of 41 degrees (SD 16.5, P<0.05). Spontaneous position elbow flexion decreased by a mean of 40 degrees (SD 21.1, P<0.05).

The Modified Ashworth score decreased significantly (P<0.05) from 3.27 (range 1 to 4) preoperatively to 0.64 (range 0 to 4) postoperatively.

The difference between the House score preoperatively and postoperatively was not significant (P=0.180). Mean patient satisfaction was 8.2/10 (SD 2.7, range 2 to 10) and mean caregiver satisfaction was 7.1/10 (SD 2.7, range 1 to 10).

Conclusion:

A combined surgical approach to elbow flexion deformity in the form of a lengthening procedure and selective neurectomy of the elbow flexors result in a significant and sustained improvement of the spontaneous position, active and passive elbow extension and elbow flexor spasticity and high patient and caregiver satisfaction.

Level of Evidence:

Case series, level IV.
KAT8 enhances the resistance of lung cancer cells to cisplatin by acetylation of PKM2
Authors: Li Zhenyu , Lu Xiangji , Zhang Jing , Liu Tao , Xu Mingzhi , Liu Shuai , Liang Junguo
Published: May 2024

Cisplatin (CDDP)-based chemotherapy resistance is a major challenge for lung cancer treatment. PKM2 is the rate-limiting enzyme of glycolysis, which is associated with CDDP resistance. KAT8 is an acetyltransferase that regulates lung cancer progression. Thus, we aimed to explore whether KAT8 regulates PKM2 acetylation to participate in CDDP resistance. CDDP resistance was analyzed by CCK-8, flow cytometry and western blotting. To explore the regulation of KAT8 on PKM2, coimmunoprecipitation (Co-IP), immunofluorescence and immunoprecipitation followed by western blotting were performed. Glycolysis was determined using glucose consumption, lactate production, ATP level detection kits and extracellular acidification rate assay. We observed that KAT8 levels were downregulated in CDDP-treated A549 and PC9 cells. Interference with KAT8 inhibited cell viability, promoted apoptosis and upregulated PARP1 and cleaved-PARP1 levels of A549 cells treated with CDDP, suggesting the sensitivity to CDDP was enhanced, while KAT8 overexpression attenuated the CDDP sensitivity. Moreover, KAT8 interacted with PKM2 to promote the PKM2 K433 acetylation. PKM2 K433 mutated plasmids inhibited the si-KAT8-regulated cell viability, apoptosis and glycolysis compared with PKM2-WT. Besides, KAT8 reversed the inhibition of tumor growth caused by CDDP. In conclusion, KAT8-mediated PKM2 K433 acetylation was associated with the resistance of lung cancer cells to CDDP. The findings may provide a new idea for the treatment of CDDP-resistant lung cancer.